sci-biology:tophat-1.0.12:20160922-133122.log

sci-biology:tophat-1.0.12:20160922-133122.log (text/plain), 65.95 KB, created by Toralf Förster on 2016-09-22 17:03:25 UTC

 * Package:    sci-biology/tophat-1.0.12
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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 <[e-mail]> 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::Tristate2>&, TValue&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/basic.h: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<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs]
  typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > 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<TSpec>&, TLeft&, TRight&)’:
./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:51:0,
                 from bwt_map.h:16,
                 from reads.cpp:20:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:53:0,
                 from bwt_map.h:16,
                 from reads.cpp:20:
./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:57:0,
                 from bwt_map.h:16,
                 from reads.cpp:20:
./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:62:0,
                 from bwt_map.h:16,
                 from reads.cpp:20:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
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::Tristate2>&, TValue&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/basic.h: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<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs]
  typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > 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<TSpec>&, TLeft&, TRight&)’:
./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:51:0,
                 from bwt_map.h:16,
                 from bwt_map.cpp:21:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:53:0,
                 from bwt_map.h:16,
                 from bwt_map.cpp:21:
./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:57:0,
                 from 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<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:62:0,
                 from bwt_map.h:16,
                 from bwt_map.cpp:21:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
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::Tristate2>&, TValue&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/basic.h: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<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs]
  typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > 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<TSpec>&, TLeft&, TRight&)’:
./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:51:0,
                 from junctions.h:22,
                 from junctions.cpp:16:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:53:0,
                 from junctions.h:22,
                 from junctions.cpp:16:
./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:57:0,
                 from junctions.h:22,
                 from junctions.cpp:16:
./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:62:0,
                 from junctions.h:22,
                 from junctions.cpp:16:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
In file included from ./SeqAn-1.1/seqan/find.h:62:0,
                 from junctions.h:23,
                 from junctions.cpp:16:
./SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function ‘void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)’:
./SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef ‘TWord’ locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^~~~~
In file included from ./SeqAn-1.1/seqan/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<TSource, TSpec>&, FastaAlign)’:
./SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
./SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function ‘void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)’:
./SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef ‘TPosition’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^~~~~~~~~
In file included from ./SeqAn-1.1/seqan/file.h:69:0,
                 from 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<TSource, TSpec>&, TStringContainer&, CGViz)’:
./SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef ‘TRow’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^~~~
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::Tristate2>&, TValue&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/basic.h: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<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs]
  typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > 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<TSpec>&, TLeft&, TRight&)’:
./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:51:0,
                 from bwt_map.h:16,
                 from fragments.cpp:15:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:53:0,
                 from bwt_map.h:16,
                 from fragments.cpp:15:
./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:57:0,
                 from bwt_map.h:16,
                 from fragments.cpp:15:
./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:62:0,
                 from bwt_map.h:16,
                 from fragments.cpp:15:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
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::Tristate2>&, TValue&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef ‘THolderType’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^~~~~~~~~~~
./SeqAn-1.1/seqan/basic/basic_holder.h: In function ‘void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)’:
./SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef ‘THostValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/basic.h: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<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/basic/basic_allocator_chunkpool.h:226:67: warning: typedef ‘TAllocator’ locally defined but not used [-Wunused-local-typedefs]
  typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > 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<TSpec>&, TLeft&, TRight&)’:
./SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef ‘TLeftValue’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^~~~~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:51:0,
                 from bwt_map.h:16,
                 from inserts.cpp:16:
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
./SeqAn-1.1/seqan/sequence/string_base.h: In function ‘void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)’:
./SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef ‘TTarget’ locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^~~~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:53:0,
                 from bwt_map.h:16,
                 from inserts.cpp:16:
./SeqAn-1.1/seqan/sequence/string_alloc.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:57:0,
                 from bwt_map.h:16,
                 from inserts.cpp:16:
./SeqAn-1.1/seqan/sequence/string_packed.h: In static member function ‘static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef ‘TIterator’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^~~~~~~~~
./SeqAn-1.1/seqan/sequence/string_packed.h: In function ‘typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)’:
./SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef ‘TSize’ locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^~~~~
In file included from ./SeqAn-1.1/seqan/sequence.h:62:0,
                 from bwt_map.h:16,
                 from inserts.cpp:16:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function ‘void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)’:
./SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef ‘TId’ locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^~~
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<unsigned int, unsigned int> Gene::coords() const’:
genes.cpp:93:52: error: no matching function for call to ‘make_pair(uint32_t&, uint32_t&)’
     return make_pair<uint32_t, uint32_t>(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<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__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<uint32_t, uint32_t>(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'