* Package:    sci-biology/bowtie-2.2.9
 * Repository: gentoo
 * Maintainer: sci-biology@gentoo.org
 * USE:        abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc kernel_linux tbb userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking bowtie2-2.2.9-source.zip to /var/tmp/portage/sci-biology/bowtie-2.2.9/work
>>> Source unpacked in /var/tmp/portage/sci-biology/bowtie-2.2.9/work
>>> Preparing source in /var/tmp/portage/sci-biology/bowtie-2.2.9/work/bowtie2-2.2.9 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/bowtie-2.2.9/work/bowtie2-2.2.9 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/bowtie-2.2.9/work/bowtie2-2.2.9 ...
make -j1 CC=x86_64-pc-linux-gnu-gcc CPP=x86_64-pc-linux-gnu-g++ CXX=x86_64-pc-linux-gnu-g++ CFLAGS= CXXFLAGS= 'EXTRA_FLAGS=-Wl,-O1 -Wl,--as-needed' 'RELEASE_FLAGS=-march=native -O2 -pipe -msse2' WITH_TBB=1 
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -msse2 -DCOMPILER_OPTIONS="\"-march=native -O2 -pipe -msse2 -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -DPOPCNT_CAPABILITY -DWITH_TBB \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`x86_64-pc-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	-lpthread -ltbb -ltbbmalloc_proxy 
In file included from blockwise_sa.h:34:0,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:27:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
blockwise_sa.h: In instantiation of ‘class KarkkainenBlockwiseSA<S2bDnaString>’:
blockwise_sa.h:520:48:   required from here
blockwise_sa.h:218:5: error: looser throw specifier for ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = S2bDnaString]’
     ~KarkkainenBlockwiseSA()
     ^
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
blockwise_sa.h:178:7: error:   overriding ‘virtual InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from bt2_build.cpp:27:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<stringstream> ss(new stringstream());
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bt2_build.cpp:27:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
blockwise_sa.h: In instantiation of ‘class KarkkainenBlockwiseSA<SString<char> >’:
bt2_idx.h:1062:66:   required from ‘void Ebwt::initFromVector(EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString<char>; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream<char>; std::__cxx11::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:655:23:   required from ‘Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString<char>; int32_t = int; std::__cxx11::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]’
bt2_build.cpp:462:14:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, int) [with TStr = SString<char>; std::__cxx11::string = std::__cxx11::basic_string<char>]’
bt2_build.cpp:618:78:   required from here
blockwise_sa.h:218:5: error: looser throw specifier for ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = SString<char>]’
     ~KarkkainenBlockwiseSA()
     ^
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
blockwise_sa.h:178:7: error:   overriding ‘virtual InorderBlockwiseSA<SString<char> >::~InorderBlockwiseSA() noexcept’
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from blockwise_sa.h:34:0,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from bt2_idx.h:42:0,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In instantiation of ‘class KarkkainenBlockwiseSA<S2bDnaString>’:
blockwise_sa.h:520:48:   required from here
blockwise_sa.h:218:5: error: looser throw specifier for ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = S2bDnaString]’
     ~KarkkainenBlockwiseSA()
     ^
In file included from bt2_idx.h:42:0,
                 from bt2_idx.cpp:25:
blockwise_sa.h:178:7: error:   overriding ‘virtual InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from bt2_idx.cpp:25:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<stringstream> ss(new stringstream());
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bt2_idx.cpp:25:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from blockwise_sa.h:34:0,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from bt2_idx.h:42:0,
                 from bt2_io.cpp:25:
blockwise_sa.h: In instantiation of ‘class KarkkainenBlockwiseSA<S2bDnaString>’:
blockwise_sa.h:520:48:   required from here
blockwise_sa.h:218:5: error: looser throw specifier for ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = S2bDnaString]’
     ~KarkkainenBlockwiseSA()
     ^
In file included from bt2_idx.h:42:0,
                 from bt2_io.cpp:25:
blockwise_sa.h:178:7: error:   overriding ‘virtual InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from bt2_io.cpp:25:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<stringstream> ss(new stringstream());
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bt2_io.cpp:25:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from blockwise_sa.h:34:0,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from bt2_idx.h:42:0,
                 from bt2_util.cpp:26:
blockwise_sa.h: In instantiation of ‘class KarkkainenBlockwiseSA<S2bDnaString>’:
blockwise_sa.h:520:48:   required from here
blockwise_sa.h:218:5: error: looser throw specifier for ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA() noexcept (false) [with TStr = S2bDnaString]’
     ~KarkkainenBlockwiseSA()
     ^
In file included from bt2_idx.h:42:0,
                 from bt2_util.cpp:26:
blockwise_sa.h:178:7: error:   overriding ‘virtual InorderBlockwiseSA<S2bDnaString>::~InorderBlockwiseSA() noexcept’
 class InorderBlockwiseSA : public BlockwiseSA<TStr> {
       ^~~~~~~~~~~~~~~~~~
In file included from bt2_util.cpp:26:0:
bt2_idx.h: In static member function ‘static std::pair<Ebwt*, Ebwt*> Ebwt::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’:
bt2_idx.h:827:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<stringstream> ss(new stringstream());
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from bt2_util.cpp:26:0:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/memory:81:0,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from multikey_qsort.h:27:0,
                 from multikey_qsort.cpp:20:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
In file included from diff_sample.cpp:20:0:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
                                ^~~~~
make: *** [Makefile:264: bowtie2-build-s] Error 1
 * ERROR: sci-biology/bowtie-2.2.9::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/bowtie-2.2.9::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/bowtie-2.2.9::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:bowtie-2.2.9:20160916-122713.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/bowtie-2.2.9/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/bowtie-2.2.9/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/bowtie-2.2.9/work/bowtie2-2.2.9'
 * S: '/var/tmp/portage/sci-biology/bowtie-2.2.9/work/bowtie2-2.2.9'