* Package: sci-biology/tophat-1.0.12 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking tophat-1.0.12.tar.gz to /var/tmp/portage/sci-biology/tophat-1.0.12/work >>> Source unpacked in /var/tmp/portage/sci-biology/tophat-1.0.12/work >>> Preparing source in /var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12 ... Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/case "\${ <-- HERE host_cpu}-\${host_os}" in/ at -e line 1. Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/case "\${host_cpu}-\${ <-- HERE host_os}" in/ at -e line 1. * Running eautoreconf in '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: tophat-1.0.12/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12 ... * econf: updating tophat-1.0.12/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating tophat-1.0.12/config/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 configure: loading site script /usr/share/config.site checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for gawk... gawk checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for perl... /usr/bin/perl checking for bash... /bin/bash checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib64/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for gzread in -lz... yes checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for int32_t... yes checking for size_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 checking dependency style of x86_64-pc-linux-gnu-g++... gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- TopHat 1.0.12 Configuration Results -- C compiler: x86_64-pc-linux-gnu-gcc -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG C++ compiler: x86_64-pc-linux-gnu-g++ -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG GCC version: x86_64-pc-linux-gnu-gcc (Gentoo 6.2.0-r1 p1.1) 6.2.0 Host System type: x86_64-pc-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12 ... make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp In file included from ./SeqAn-1.1/seqan/basic.h:64:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/basic.h:69:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h: In function ‘void seqan::deallocate(seqan::Allocator >&, TValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs] typedef Allocator > TAllocator; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:38:0, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:51:0, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:53:0, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:57:0, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:62:0, from bwt_map.h:16, from reads.cpp:20: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ mv -f .deps/reads.Tpo .deps/reads.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c mv -f .deps/alphabet.Tpo .deps/alphabet.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT bwt_map.o -MD -MP -MF .deps/bwt_map.Tpo -c -o bwt_map.o bwt_map.cpp In file included from ./SeqAn-1.1/seqan/basic.h:64:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/basic.h:69:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h: In function ‘void seqan::deallocate(seqan::Allocator >&, TValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs] typedef Allocator > TAllocator; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:38:0, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:51:0, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:53:0, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:57:0, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:62:0, from bwt_map.h:16, from bwt_map.cpp:21: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ mv -f .deps/bwt_map.Tpo .deps/bwt_map.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp mv -f .deps/common.Tpo .deps/common.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT junctions.o -MD -MP -MF .deps/junctions.Tpo -c -o junctions.o junctions.cpp In file included from ./SeqAn-1.1/seqan/basic.h:64:0, from ./SeqAn-1.1/seqan/sequence.h:27, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/basic.h:69:0, from ./SeqAn-1.1/seqan/sequence.h:27, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h: In function ‘void seqan::deallocate(seqan::Allocator >&, TValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs] typedef Allocator > TAllocator; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:38:0, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:51:0, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:53:0, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:57:0, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:62:0, from junctions.h:22, from junctions.cpp:16: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ In file included from ./SeqAn-1.1/seqan/find.h:62:0, from junctions.h:23, from junctions.cpp:16: ./SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function ‘void seqan::_patternInit(seqan::Pattern >&)’: ./SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef ‘TWord’ locally defined but not used [-Wunused-local-typedefs] typedef unsigned int TWord; ^~~~~ In file included from ./SeqAn-1.1/seqan/file.h:66:0, from junctions.h:24, from junctions.cpp:16: ./SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::read(TFile&, seqan::Align&, FastaAlign)’: ./SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ ./SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, FastaAlign)’: ./SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs] typedef typename Position::Type TPosition; ^~~~~~~~~ In file included from ./SeqAn-1.1/seqan/file.h:69:0, from junctions.h:24, from junctions.cpp:16: ./SeqAn-1.1/seqan/file/file_format_cgviz.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align&, TStringContainer&, CGViz)’: ./SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs] typedef typename Row::Type TRow; ^~~~ mv -f .deps/junctions.Tpo .deps/junctions.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT regexp.o -MD -MP -MF .deps/regexp.Tpo -c -o regexp.o `test -f 'FSA/regexp.cc' || echo './'`FSA/regexp.cc mv -f .deps/regexp.Tpo .deps/regexp.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o `test -f 'FSA/gff.cc' || echo './'`FSA/gff.cc mv -f .deps/gff.Tpo .deps/gff.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT misc.o -MD -MP -MF .deps/misc.Tpo -c -o misc.o `test -f 'FSA/misc.cc' || echo './'`FSA/misc.cc mv -f .deps/misc.Tpo .deps/misc.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o `test -f 'FSA/sequence.cc' || echo './'`FSA/sequence.cc mv -f .deps/sequence.Tpo .deps/sequence.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT fsa_alphabet.o -MD -MP -MF .deps/fsa_alphabet.Tpo -c -o fsa_alphabet.o `test -f 'FSA/fsa_alphabet.cc' || echo './'`FSA/fsa_alphabet.cc mv -f .deps/fsa_alphabet.Tpo .deps/fsa_alphabet.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT fragments.o -MD -MP -MF .deps/fragments.Tpo -c -o fragments.o fragments.cpp In file included from ./SeqAn-1.1/seqan/basic.h:64:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/basic.h:69:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h: In function ‘void seqan::deallocate(seqan::Allocator >&, TValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs] typedef Allocator > TAllocator; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:38:0, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:51:0, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:53:0, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:57:0, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:62:0, from bwt_map.h:16, from fragments.cpp:15: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ mv -f .deps/fragments.Tpo .deps/fragments.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp mv -f .deps/tokenize.Tpo .deps/tokenize.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT inserts.o -MD -MP -MF .deps/inserts.Tpo -c -o inserts.o inserts.cpp In file included from ./SeqAn-1.1/seqan/basic.h:64:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::setValue(seqan::Holder&, TValue&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference >::Type seqan::value(seqan::Holder&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THolderType; ^~~~~~~~~~~ ./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder&, const TSource&)’: ./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value >::Type THostValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/basic.h:69:0, from ./SeqAn-1.1/seqan/sequence.h:27, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h: In function ‘void seqan::deallocate(seqan::Allocator >&, TValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs] typedef Allocator > TAllocator; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:38:0, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/sequence/lexical.h: In function ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&)’: ./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs] typedef typename Value::Type TLeftValue; ^~~~~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:51:0, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSource&, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String&, const TSourceValue*, TSize, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String&, TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSource&, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ ./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String&, typename seqan::Size >::Type, typename seqan::Size >::Type, const TSourceValue*, typename seqan::Size >::Type, seqan::Tag)’: ./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs] typedef String TTarget; ^~~~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:53:0, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:57:0, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size::Type seqan::_ClearSpace_String_Packed_::_clearSpace_(T&, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type, typename seqan::Size::Type)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs] typedef typename Iterator::Type TIterator; ^~~~~~~~~ ./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size > >::Type seqan::reserve(seqan::String >&, _TSize, Insist)’: ./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs] typedef typename Size< String > >::Type TSize; ^~~~~ In file included from ./SeqAn-1.1/seqan/sequence.h:62:0, from bwt_map.h:16, from inserts.cpp:16: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet > >&, seqan::StringSet > >&, TIds, TLength)’: ./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs] typedef typename Id::Type TId; ^~~ mv -f .deps/inserts.Tpo .deps/inserts.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -I./SeqAn-1.1 -Wall -g -O3 -march=native -O2 -pipe -DNDEBUG -MT genes.o -MD -MP -MF .deps/genes.Tpo -c -o genes.o genes.cpp genes.cpp: In member function ‘std::pair Gene::coords() const’: genes.cpp:93:52: error: no matching function for call to ‘make_pair(uint32_t&, uint32_t&)’ return make_pair(start, end); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/utility:70:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/algorithm:60, from genes.cpp:13: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: candidate: template constexpr std::pair::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&) make_pair(_T1&& __x, _T2&& __y) ^~~~~~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/stl_pair.h:425:5: note: template argument deduction/substitution failed: genes.cpp:93:52: note: cannot convert ‘start’ (type ‘uint32_t {aka unsigned int}’) to type ‘unsigned int&&’ return make_pair(start, end); ^ make[2]: *** [Makefile:879: genes.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12/src' make[1]: *** [Makefile:384: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12' make: *** [Makefile:325: all] Error 2 emake failed * ERROR: sci-biology/tophat-1.0.12::gentoo failed (compile phase): * emake failed * * Call stack: * ebuild.sh, line 115: Called src_compile * environment, line 1550: Called default * phase-functions.sh, line 805: Called default_src_compile * phase-functions.sh, line 842: Called __eapi2_src_compile * phase-helpers.sh, line 785: Called die * The specific snippet of code: * emake || die "emake failed" * * If you need support, post the output of `emerge --info '=sci-biology/tophat-1.0.12::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/tophat-1.0.12::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:tophat-1.0.12:20160922-133122.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/tophat-1.0.12/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/tophat-1.0.12/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12' * S: '/var/tmp/portage/sci-biology/tophat-1.0.12/work/tophat-1.0.12'