FreeBSD Bugzilla – Attachment 167716 Details for
Bug 206939
[NEW PORT] biology/bowtie: Ultrafast, memory-efficient short read aligner
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Poudriere log
bowtie-1.1.2.log-9-3-amd64 (text/plain), 329.20 KB, created by
Jason W. Bacon
on 2016-03-04 15:40:29 UTC
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Description:
Poudriere log
Filename:
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Creator:
Jason W. Bacon
Created:
2016-03-04 15:40:29 UTC
Size:
329.20 KB
patch
obsolete
>build started at Fri Mar 4 09:12:39 CST 2016 >port directory: /usr/ports/biology/bowtie >building for: FreeBSD 9-3-amd64-default 9.3-RELEASE-p36 FreeBSD 9.3-RELEASE-p36 amd64 >maintained by: bacon4000@gmail.com >ident warning: no id keywords in /usr/local/poudriere/data/.m/9-3-amd64-default/ref//usr/ports/biology/bowtie/Makefile >Makefile ident: >Poudriere version: 3.1.12 >Host OSVERSION: 1001000 >Jail OSVERSION: 903000 > >---Begin Environment--- >PKGREPOSITORY=/tmp/pkgs >PACKAGES=/tmp/pkgs >UNAME_v=FreeBSD 9.3-RELEASE-p36 >UNAME_r=9.3-RELEASE-p36 >BLOCKSIZE=K >MAIL=/var/mail/root >STATUS=1 >WARNING_WAIT=0 >SAVED_TERM=xterm >NO_WARNING_PKG_INSTALL_EOL=yes >MASTERMNT=/usr/local/poudriere/data/.m/9-3-amd64-default/ref >FORCE_PACKAGE=yes >PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin >POUDRIERE_BUILD_TYPE=bulk >OLDPWD=/usr/home/bacon >PWD=/ >MASTERNAME=9-3-amd64-default >SCRIPTPREFIX=/usr/local/share/poudriere >USER=root >HOME=/root >POUDRIERE_VERSION=3.1.12 >SCRIPTPATH=/usr/local/share/poudriere/testport.sh >TRYBROKEN=yes >LIBEXECPREFIX=/usr/local/libexec/poudriere >LOCALBASE=/usr/local >PACKAGE_BUILDING=yes >DEV_WARNING_WAIT=0 >OSVERSION=903000 >---End Environment--- > >---Begin OPTIONS List--- >---End OPTIONS List--- > >--CONFIGURE_ARGS-- > >--End CONFIGURE_ARGS-- > >--CONFIGURE_ENV-- >MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh >--End CONFIGURE_ENV-- > >--MAKE_ENV-- >XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc48" CFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" >--End MAKE_ENV-- > >--PLIST_SUB-- >OSREL=9.3 >PREFIX=%D >LOCALBASE=/usr/local >RESETPREFIX=/usr/local >PORTDOCS="" >PORTEXAMPLES="" >LIB32DIR=lib >PERL_VERSION=5.20.3 >PERL_VER=5.20 >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/5.20 >DOCSDIR="share/doc/bowtie" >EXAMPLESDIR="share/examples/bowtie" >DATADIR="share/bowtie" >WWWDIR="www/bowtie" >ETCDIR="etc/bowtie" >--End PLIST_SUB-- > >--SUB_LIST-- >PREFIX=/usr/local >LOCALBASE=/usr/local >DATADIR=/usr/local/share/bowtie >DOCSDIR=/usr/local/share/doc/bowtie >EXAMPLESDIR=/usr/local/share/examples/bowtie >WWWDIR=/usr/local/www/bowtie >ETCDIR=/usr/local/etc/bowtie >--End SUB_LIST-- > >---Begin make.conf--- >USE_PACKAGE_DEPENDS=yes >BATCH=yes >WRKDIRPREFIX=/wrkdirs >PORTSDIR=/usr/ports >PACKAGES=/packages >DISTDIR=/distfiles >---End make.conf--- >=======================<phase: check-sanity >============================ >===> License ART10 accepted by the user >=========================================================================== >=======================<phase: pkg-depends >============================ >===> bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - not found >===> Installing existing package /packages/All/pkg-1.6.4_1.txz >[9-3-amd64-default] Installing pkg-1.6.4_1... >[9-3-amd64-default] Extracting pkg-1.6.4_1: .......... done >===> bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found >===> Returning to build of bowtie-1.1.2 >=========================================================================== >=======================<phase: fetch-depends >============================ >=========================================================================== >=======================<phase: fetch >============================ >===> License ART10 accepted by the user >===> bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by bowtie-1.1.2 for building >=========================================================================== >=======================<phase: checksum >============================ >===> License ART10 accepted by the user >===> bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by bowtie-1.1.2 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 >===> bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found >===> Fetching all distfiles required by bowtie-1.1.2 for building >===> Extracting for bowtie-1.1.2 >=> SHA256 Checksum OK for BenLangmead-bowtie-v1.1.2_GH0.tar.gz. >=========================================================================== >=======================<phase: patch-depends >============================ >=========================================================================== >=======================<phase: patch >============================ >===> Patching for bowtie-1.1.2 >===> Applying FreeBSD patches for bowtie-1.1.2 >=========================================================================== >=======================<phase: build-depends >============================ >===> bowtie-1.1.2 depends on executable: gmake - not found >===> Installing existing package /packages/All/gmake-4.1_2.txz >[9-3-amd64-default] Installing gmake-4.1_2... >[9-3-amd64-default] `-- Installing indexinfo-0.2.4... >[9-3-amd64-default] `-- Extracting indexinfo-0.2.4: .... done >[9-3-amd64-default] `-- Installing libiconv-1.14_9... >[9-3-amd64-default] `-- Extracting libiconv-1.14_9: .......... done >[9-3-amd64-default] `-- Installing gettext-runtime-0.19.7... >[9-3-amd64-default] `-- Extracting gettext-runtime-0.19.7: .......... done >[9-3-amd64-default] Extracting gmake-4.1_2: .......... done >===> bowtie-1.1.2 depends on executable: gmake - found >===> Returning to build of bowtie-1.1.2 >===> bowtie-1.1.2 depends on executable: gcc48 - not found >===> Installing existing package /packages/All/gcc-4.8.5_2.txz >[9-3-amd64-default] Installing gcc-4.8.5_2... >[9-3-amd64-default] `-- Installing mpc-1.0.3... >[9-3-amd64-default] | `-- Installing gmp-5.1.3_3... >[9-3-amd64-default] | `-- Extracting gmp-5.1.3_3: .......... done >[9-3-amd64-default] | `-- Installing mpfr-3.1.3_1... >[9-3-amd64-default] | `-- Extracting mpfr-3.1.3_1: .......... done >[9-3-amd64-default] `-- Extracting mpc-1.0.3: ...... done >[9-3-amd64-default] `-- Installing gcc-ecj-4.5... >[9-3-amd64-default] `-- Extracting gcc-ecj-4.5: . done >[9-3-amd64-default] `-- Installing binutils-2.25.1,1... >[9-3-amd64-default] `-- Extracting binutils-2.25.1,1: .......... done >[9-3-amd64-default] Extracting gcc-4.8.5_2: .......... done >Message from gcc-4.8.5_2: >To ensure binaries built with this toolchain find appropriate versions >of the necessary run-time libraries, you may want to link using > > -Wl,-rpath=/usr/local/lib/gcc48 > >For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens >transparently. >===> bowtie-1.1.2 depends on executable: gcc48 - found >===> Returning to build of bowtie-1.1.2 >===> bowtie-1.1.2 depends on file: /usr/local/bin/as - found >=========================================================================== >=======================<phase: lib-depends >============================ >=========================================================================== >====>> Recording filesystem state for prebuild... done >=======================<phase: configure >============================ >===> bowtie-1.1.2 depends on executable: gmake - found >===> bowtie-1.1.2 depends on executable: gcc48 - found >===> bowtie-1.1.2 depends on file: /usr/local/bin/as - found >===> Configuring for bowtie-1.1.2 >=========================================================================== >=======================<phase: build >============================ >===> Building for bowtie-1.1.2 >g++48 -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >g++48 -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >g++48 -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >g++48 -O -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/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::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/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::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/find.h:62:0, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)': >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:62:0, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)': >SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] > typedef unsigned int TWord; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ebwt_search.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ebwt_search.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ebwt_search.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ebwt_search.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from ebwt_build.cpp:7: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from ebwt_build.cpp:7: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from ebwt_build.cpp:7: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from ebwt_build.cpp:7: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt.h:16, > from ebwt_search.cpp:14: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt.h:16, > from ebwt_search.cpp:14: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt.h:16, > from ebwt_search.cpp:14: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt.h:16, > from ebwt_search.cpp:14: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >In file included from ebwt.h:27:0, > from ebwt_build.cpp:11: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_build.cpp:11: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_build.cpp:11: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_build.cpp:11: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_search.cpp:14: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_search.cpp:14: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_search.cpp:14: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from ebwt_search.cpp:14: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:40:0, > from ebwt_build.cpp:11: >reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': >reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] > uint64_t origBufOff = bufOff; > ^ >reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] > bool binarySearched = false; > ^ >In file included from ebwt.h:40:0, > from ebwt_build.cpp:11: >reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': >reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] > uint64_t origBufOff = bufOff; > ^ >reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] > bool binarySearched = false; > ^ >In file included from ebwt.h:40:0, > from ebwt_search.cpp:14: >reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': >reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] > uint64_t origBufOff = bufOff; > ^ >reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] > bool binarySearched = false; > ^ >In file included from ebwt.h:40:0, > from ebwt_search.cpp:14: >reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': >reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] > uint64_t origBufOff = bufOff; > ^ >reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable] > bool binarySearched = false; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] > VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/index.h:27, > from ebwt_build.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-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::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:731:88: required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]' >ebwt.h:4032:32: required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = unsigned int; uint32_t = unsigned int]' >ebwt_build.cpp:485:9: required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]' >ebwt_build.cpp:622:69: required from here >SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:731:88: required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]' >ebwt.h:4032:32: required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = long unsigned int; uint32_t = unsigned int]' >ebwt_build.cpp:485:9: required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]' >ebwt_build.cpp:622:69: required from here >SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] > VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from ebwt_search.cpp:8: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-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:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >g++48 -O \ > -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >g++48 -O \ > -DCOMPILER_OPTIONS="\"-O -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \"" -DPOPCNT_CAPABILITY -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48 \ > -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++48 -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 \ > -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48 -lpthread >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/find.h:62:0, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)': >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/sequence.h:62:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/find.h:62:0, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)': >SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] > typedef unsigned int TWord; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt.h:16, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt.h:16, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:82:0, > from ebwt.h:16, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, 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<TValue, SimpleShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, 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<TValue, FixedShape<q> > >::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<TValue, FixedShape<q> > >::Type TSize; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, 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<TValue, TSpec> >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/index.h:83:0, > from ebwt.h:16, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, 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<TValue, GappedShape> >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, 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<TValue, FixedGappedShape<TSpec> > >::Type THValue; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ebwt.h:24, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ebwt.h:24, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ebwt.h:24, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ebwt.h:24, > from bowtie_inspect.cpp:10: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from ebwt.h:27:0, > from bowtie_inspect.cpp:10: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from bowtie_inspect.cpp:10: >blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()': >blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from bowtie_inspect.cpp:10: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from ebwt.h:27:0, > from bowtie_inspect.cpp:10: >blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()': >blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<TStr>::Type TAlphabet; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] > VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from SeqAn-1.1/seqan/find.h:31, > from bowtie_inspect.cpp:6: >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:906:102: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_packed.h:1237:40: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]' >SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::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<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-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::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:509:6: required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_base.h:1429:52: required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_base.h:1459:67: required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]' >ebwt.h:2965:35: required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]' >bowtie_inspect.cpp:283:2: required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]' >bowtie_inspect.cpp:461:42: required from here >SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] >SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >': >SeqAn-1.1/seqan/sequence/string_packed.h:509:6: required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_base.h:1429:52: required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]' >SeqAn-1.1/seqan/sequence/string_base.h:1459:67: required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]' >ebwt.h:2965:35: required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]' >bowtie_inspect.cpp:283:2: required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]' >bowtie_inspect.cpp:461:42: required from here >SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare] >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from pat.cpp:5: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from pat.cpp:5: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from pat.cpp:5: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from pat.cpp:6: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from pat.cpp:6: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from pat.cpp:6: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from pat.cpp:6: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ebwt_search_util.h:8, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit.h:12, > from ebwt_search_util.h:9, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit.h:12, > from ebwt_search_util.h:9, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit.h:12, > from ebwt_search_util.h:9, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit.h:12, > from ebwt_search_util.h:9, > from ebwt_search_util.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from ref_read.h:11, > from ref_read.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from ref_read.h:12, > from ref_read.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit_set.cpp:10: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit_set.cpp:10: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from hit_set.cpp:10: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit_set.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit_set.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit_set.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit_set.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from pat.h:12, > from sam.cpp:11: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from pat.h:13, > from sam.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from pat.h:13, > from sam.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from pat.h:13, > from sam.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from pat.h:13, > from sam.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from alphabet.h:6, > from color_dec.cpp:11: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from color_dec.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from color_dec.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from color_dec.cpp:11: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from color_dec.cpp:11: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/basic.h:64:0, > from SeqAn-1.1/seqan/sequence.h:27, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)': >SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] > typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType; > ^ >SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, 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<Holder<TValue, Tristate2> >::Type THostValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:38:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, 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<TLeft>::Type TLeftValue; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:51:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)': >SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] > typedef String<TTargetValue, TTargetSpec> TTarget; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:53:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:57:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::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<T, Standard>::Type TIterator; > ^ >SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _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<TValue, Alloc<TSpec> > >::Type TSize; > ^ >In file included from SeqAn-1.1/seqan/sequence.h:62:0, > from hit.h:11, > from hit.cpp:1: >SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, 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<TStringSet>::Type TId; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >In file included from SeqAn-1.1/seqan/file.h:66:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TPosition; > ^ >In file included from SeqAn-1.1/seqan/file.h:69:0, > from alphabet.h:7, > from hit.h:12, > from hit.cpp:1: >SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, 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<TAlign>::Type TRow; > ^ >=========================================================================== >====>> Checking for filesystem violations... done >=======================<phase: run-depends >============================ >===> bowtie-1.1.2 depends on executable: webbrowser - not found >===> Installing existing package /packages/All/webbrowser-0.3.txz >[9-3-amd64-default] Installing webbrowser-0.3... >[9-3-amd64-default] Extracting webbrowser-0.3: ..... done >===> bowtie-1.1.2 depends on executable: webbrowser - found >===> Returning to build of bowtie-1.1.2 >===> bowtie-1.1.2 depends on executable: gcc48 - found >===> bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - not found >===> Installing existing package /packages/All/perl5-5.20.3_8.txz >[9-3-amd64-default] Installing perl5-5.20.3_8... >[9-3-amd64-default] Extracting perl5-5.20.3_8: .......... done >Message from perl5-5.20.3_8: >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 depends on package: perl5>=5.20<5.21 - found >===> Returning to build of bowtie-1.1.2 >=========================================================================== >====>> Recording filesystem state for prestage... done >=======================<phase: stage >============================ >===> Staging for bowtie-1.1.2 >===> bowtie-1.1.2 depends on executable: webbrowser - found >===> bowtie-1.1.2 depends on executable: gcc48 - found >===> bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found >===> Generating temporary packing list >mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin >for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \ > cp -f $file /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin ; \ >done >/bin/mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie/scripts >install -m 555 /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-build /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-inspect /usr/ports/biology/bowtie/files/bowtie-manual /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin >install -m 555 /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.sh /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.pl /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie/scripts >cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2 && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- 'genomes indexes reads' /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie >cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/doc && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- \* /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/doc/bowtie >/usr/bin/strip /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin/*-[sl] >====> Compressing man pages (compress-man) >=========================================================================== >====> Running Q/A tests (stage-qa) >====> Checking for pkg-plist issues (check-plist) >===> Parsing plist >===> Checking for items in STAGEDIR missing from pkg-plist >===> Checking for items in pkg-plist which are not in STAGEDIR >===> No pkg-plist issues found (check-plist) >====>> Checking for staging violations... done >=======================<phase: package >============================ >===> Building package for bowtie-1.1.2 >=========================================================================== >=======================<phase: install-mtree >============================ >=========================================================================== >====>> Recording filesystem state for preinst... done >=======================<phase: install >============================ >===> Installing for bowtie-1.1.2 >===> bowtie-1.1.2 depends on executable: webbrowser - found >===> bowtie-1.1.2 depends on executable: gcc48 - found >===> bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found >===> Checking if bowtie already installed >===> Registering installation for bowtie-1.1.2 >[9-3-amd64-default] Installing bowtie-1.1.2... >=========================================================================== >====>> Checking shared library dependencies > 0x0000000000000001 (NEEDED) Shared library: [libc.so.7] > 0x0000000000000001 (NEEDED) Shared library: [libgcc_s.so.1] > 0x0000000000000001 (NEEDED) Shared library: [libm.so.5] > 0x0000000000000001 (NEEDED) Shared library: [libstdc++.so.6] > 0x0000000000000001 (NEEDED) Shared library: [libthr.so.3] >=======================<phase: deinstall >============================ >===> Deinstalling for bowtie >===> Deinstalling bowtie-1.1.2 >Updating database digests format: .......... done >Checking integrity... done (0 conflicting) >Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): > >Installed packages to be REMOVED: > bowtie-1.1.2 > >The operation will free 14 MiB. >[9-3-amd64-default] [1/1] Deinstalling bowtie-1.1.2... >[9-3-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done >=========================================================================== >====>> Checking for extra files and directories >[00:01:11] ====>> Installing from package >[9-3-amd64-default] Installing bowtie-1.1.2... >[9-3-amd64-default] Extracting bowtie-1.1.2: .......... done >[00:01:11] ====>> Cleaning up >===> Cleaning for bowtie-1.1.2 >[00:01:12] ====>> Deinstalling package >Updating database digests format: . done >Checking integrity... done (0 conflicting) >Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): > >Installed packages to be REMOVED: > bowtie-1.1.2 > >The operation will free 14 MiB. >[9-3-amd64-default] [1/1] Deinstalling bowtie-1.1.2... >[9-3-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done >build of biology/bowtie ended at Fri Mar 4 09:13:44 CST 2016 >build time: 00:01:05
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