Mock Version: 1.4.9 Mock Version: 1.4.9 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/bowtie.spec'], chrootPath='/var/lib/mock/f29-build-26204-13601/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/bowtie.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False BUILDSTDERR: warning: Macro expanded in comment on line 12: %{name}-script-shebang.patch BUILDSTDERR: warning: Macro expanded in comment on line 13: %{name}-gcc47.patch Building target platforms: riscv64 Building for target riscv64 Wrote: /builddir/build/SRPMS/bowtie-1.0.1-11.fc29.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bowtie.spec'], chrootPath='/var/lib/mock/f29-build-26204-13601/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/bowtie.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False BUILDSTDERR: warning: Macro expanded in comment on line 12: %{name}-script-shebang.patch BUILDSTDERR: warning: Macro expanded in comment on line 13: %{name}-gcc47.patch Building target platforms: riscv64 Building for target riscv64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.qDKpnv + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bowtie-1.0.1 + /usr/bin/unzip -qq /builddir/build/SOURCES/bowtie-1.0.1-src.zip + STATUS=0 + '[' 0 -ne 0 ']' + cd bowtie-1.0.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (bowtie-arm-gcc.patch):' Patch #0 (bowtie-arm-gcc.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .bowtie-arm-gcc.patch --fuzz=0 patching file Makefile + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.hBLFdT + umask 022 + cd /builddir/build/BUILD + cd bowtie-1.0.1 + make -j4 -p 'EXTRA_FLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 -I third_party \ -o bowtie-build ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \ -lpthread g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \ -I SeqAn-1.1 -I third_party \ -o bowtie ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lpthread g++ -O3 \ -DCOMPILER_OPTIONS="\"-O3 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \"" -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \ -I SeqAn-1.1 -I third_party -I . \ -o bowtie-inspect bowtie_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \ -lpthread BUILDSTDERR: /bin/sh: hostname: command not found BUILDSTDERR: /bin/sh: hostname: command not found BUILDSTDERR: /bin/sh: hostname: command not found BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:64, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THostValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:64, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THostValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:64, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder&, TValue&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference >::Type seqan::value(seqan::Holder&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THolderType; BUILDSTDERR: ^~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder&, const TSource&)': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value >::Type THostValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:38, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TLeftValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:51, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:53, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:57, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Iterator::Type TIterator; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:62, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Id::Type TId; BUILDSTDERR: ^~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:38, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TLeftValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:38, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TLeftValue; BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:51, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:51, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:53, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef String TTarget; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:53, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:57, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Iterator::Type TIterator; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:57, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Iterator::Type TIterator; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< String > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:62, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Id::Type TId; BUILDSTDERR: ^~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:62, BUILDSTDERR: from SeqAn-1.1/seqan/find.h:31, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)': BUILDSTDERR: SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Id::Type TId; BUILDSTDERR: ^~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/find.h:62, BUILDSTDERR: from bowtie_inspect.cpp:6: BUILDSTDERR: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': BUILDSTDERR: SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef unsigned int TWord; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/find.h:62, BUILDSTDERR: from ebwt_search.cpp:8: BUILDSTDERR: SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern >&)': BUILDSTDERR: SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef unsigned int TWord; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:82, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< Shape > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:83, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:66, BUILDSTDERR: from ebwt_build.cpp:7: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Position::Type TPosition; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:66, BUILDSTDERR: from alphabet.h:7, BUILDSTDERR: from ebwt_search.cpp:11: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Position::Type TPosition; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:69, BUILDSTDERR: from ebwt_build.cpp:7: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:69, BUILDSTDERR: from alphabet.h:7, BUILDSTDERR: from ebwt_search.cpp:11: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:82, BUILDSTDERR: from ebwt.h:16, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< Shape > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:83, BUILDSTDERR: from ebwt.h:16, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:66, BUILDSTDERR: from alphabet.h:7, BUILDSTDERR: from ebwt.h:24, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Position::Type TPosition; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/file.h:69, BUILDSTDERR: from alphabet.h:7, BUILDSTDERR: from ebwt.h:24, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)': BUILDSTDERR: SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Row::Type TRow; BUILDSTDERR: ^~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:82, BUILDSTDERR: from ebwt.h:16, BUILDSTDERR: from ebwt_search.cpp:14: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Size< Shape > >::Type TSize; BUILDSTDERR: ^~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hashUpper(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value >::Type seqan::hash2(seqan::Shape&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/index.h:83, BUILDSTDERR: from ebwt.h:16, BUILDSTDERR: from ebwt_search.cpp:14: BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > > >::Type seqan::hash(seqan::Shape > >&, TIter)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hash(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value > >::Type seqan::hashUpper(seqan::Shape >&, TIter, TSize)': BUILDSTDERR: SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value< Shape > >::Type THValue; BUILDSTDERR: ^~~~~~~ BUILDSTDERR: In file included from blockwise_sa.h:13, BUILDSTDERR: from ebwt.h:27, BUILDSTDERR: from ebwt_build.cpp:11: BUILDSTDERR: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': BUILDSTDERR: diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from ebwt.h:27, BUILDSTDERR: from ebwt_build.cpp:11: BUILDSTDERR: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': BUILDSTDERR: blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~ BUILDSTDERR: blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~~ BUILDSTDERR: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': BUILDSTDERR: blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': BUILDSTDERR: blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from blockwise_sa.h:13, BUILDSTDERR: from ebwt.h:27, BUILDSTDERR: from ebwt_search.cpp:14: BUILDSTDERR: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': BUILDSTDERR: diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from ebwt.h:27, BUILDSTDERR: from ebwt_search.cpp:14: BUILDSTDERR: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': BUILDSTDERR: blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~ BUILDSTDERR: blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~~ BUILDSTDERR: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': BUILDSTDERR: blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': BUILDSTDERR: blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from ebwt_build.cpp:11: BUILDSTDERR: ebwt.h: In destructor 'Ebwt::~Ebwt()': BUILDSTDERR: ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~~~~~ BUILDSTDERR: ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~~~ BUILDSTDERR: ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from ebwt_search.cpp:14: BUILDSTDERR: ebwt.h: In destructor 'Ebwt::~Ebwt()': BUILDSTDERR: ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~~~~~ BUILDSTDERR: ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~~~ BUILDSTDERR: ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from blockwise_sa.h:13, BUILDSTDERR: from ebwt.h:27, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': BUILDSTDERR: diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d1]) diffCnt++; diffs[d1] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~ BUILDSTDERR: diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(!diffs[d2]) diffCnt++; diffs[d2] = true; BUILDSTDERR: ^~~~~ BUILDSTDERR: In file included from ebwt.h:27, BUILDSTDERR: from bowtie_inspect.cpp:10: BUILDSTDERR: blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()': BUILDSTDERR: blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~ BUILDSTDERR: blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample BUILDSTDERR: ^~~ BUILDSTDERR: blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::buildSamples()': BUILDSTDERR: blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA::nextBlock()': BUILDSTDERR: blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs] BUILDSTDERR: typedef typename Value::Type TAlphabet; BUILDSTDERR: ^~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/sequence.h:57, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:906:43: required from 'typename seqan::Position > >::Type seqan::position(const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Position > >::Type = long unsigned int]' BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference > >::Type seqan::operator-(const seqan::Iter >&, const seqan::Iter >&) [with TContainer = const seqan::String, seqan::Packed<> >; THostspec = seqan::Alloc; typename seqan::Difference > >::Type = long int]' BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size >::Type seqan::length(const seqan::String&) [with TValue = seqan::SimpleType; TSpec = seqan::Packed<>; typename seqan::Size >::Type = long unsigned int]' BUILDSTDERR: blockwise_sa.h:354:42: required from here BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] BUILDSTDERR: VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE), BUILDSTDERR: ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts, seqan::Packed<> > >': BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:731:75: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' BUILDSTDERR: ebwt.h:4022:9: required from 'static TStr Ebwt::join(std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t) [with TStr = seqan::String, seqan::Packed<> >; uint32_t = unsigned int]' BUILDSTDERR: ebwt_build.cpp:453:36: required from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Packed<> >; std::__cxx11::string = std::__cxx11::basic_string]' BUILDSTDERR: ebwt_build.cpp:595:69: required from here BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue >::' and 'enum seqan::BitsPerValue::' [-Wenum-compare] BUILDSTDERR: In file included from bowtie_inspect.cpp:10: BUILDSTDERR: ebwt.h: In destructor 'Ebwt::~Ebwt()': BUILDSTDERR: ebwt.h:802:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:802:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_fchr != NULL) delete[] _fchr; _fchr = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:803:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:803:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_ftab != NULL) delete[] _ftab; _ftab = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:804:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:804:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_eftab != NULL) delete[] _eftab; _eftab = NULL; BUILDSTDERR: ^~~~~~ BUILDSTDERR: ebwt.h:810:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:810:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_isa != NULL) delete[] _isa; _isa = NULL; BUILDSTDERR: ^~~~ BUILDSTDERR: ebwt.h:811:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:811:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_plen != NULL) delete[] _plen; _plen = NULL; BUILDSTDERR: ^~~~~ BUILDSTDERR: ebwt.h:812:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~ BUILDSTDERR: ebwt.h:812:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL; BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:101, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]': BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]' BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]' BUILDSTDERR: SeqAn-1.1/seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = void; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size > >::Type = long unsigned int]' BUILDSTDERR: ebwt.h:4022:9: required from 'static TStr Ebwt::join(std::vector&, std::vector&, uint32_t, const RefReadInParams&, uint32_t) [with TStr = seqan::String, seqan::Alloc >; uint32_t = unsigned int]' BUILDSTDERR: ebwt_build.cpp:453:36: required from 'void driver(const string&, std::vector >&, const string&, bool) [with TStr = seqan::String, seqan::Alloc >; std::__cxx11::string = std::__cxx11::basic_string]' BUILDSTDERR: ebwt_build.cpp:584:61: required from here BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] BUILDSTDERR: memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); BUILDSTDERR: ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:106, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType' declared here BUILDSTDERR: struct SimpleType BUILDSTDERR: ^~~~~~~~~~ BUILDSTDERR: In file included from SeqAn-1.1/seqan/basic.h:101, BUILDSTDERR: from SeqAn-1.1/seqan/sequence.h:27, BUILDSTDERR: from SeqAn-1.1/seqan/index.h:27, BUILDSTDERR: from ebwt_build.cpp:5: BUILDSTDERR: SeqAn-1.1/seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType

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