sci-biology:bowtie-2.2.9:20200513-162919.log

sci-biology:bowtie-2.2.9:20200513-162919.log (text/plain), 25.23 KB, created by Toralf Förster on 2020-05-13 17:24:04 UTC

 * Package:    sci-biology/bowtie-2.2.9
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc kernel_linux tbb userland_GNU
 * FEATURES:   network-sandbox 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 ...
 * Applying bowtie-2.2.9-fix-c++14.patch ...
 [ ok ]
>>> 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 -Wl,--defsym=__gentoo_check_ldflags__=0' 'RELEASE_FLAGS=-O2 -pipe -march=native  -msse2' WITH_TBB=1 
x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native  -msse2 -DCOMPILER_OPTIONS="\"-O2 -pipe -march=native  -msse2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -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 bt2_idx.h:59,
                 from bt2_build.cpp:27:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                      ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
   52 |        std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                                                                     ^

In file included from blockwise_sa.h:24,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:27:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:27:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from blockwise_sa.h:34,
                 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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_build.cpp:27:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_build.cpp:27:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_build.cpp:27:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from threading.h:26,
                 from ds.h:30,
                 from ref_read.h:33,
                 from ref_read.cpp:20:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from edit.h:29,
                 from edit.cpp:21:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from bt2_idx.h:59,
                 from bt2_idx.cpp:25:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                      ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
   52 |        std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                                                                     ^

In file included from blockwise_sa.h:24,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_idx.cpp:25:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from blockwise_sa.h:34,
                 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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_idx.cpp:25:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_idx.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_idx.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_idx.h:59,
                 from bt2_io.cpp:25:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                      ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
   52 |        std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                                                                     ^

In file included from blockwise_sa.h:24,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_io.cpp:25:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from blockwise_sa.h:34,
                 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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_io.cpp:25:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_io.cpp:25:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_io.cpp:25:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_idx.h:59,
                 from bt2_util.cpp:26:
processor_support.h:52:22: error: extended character “ is not valid in an identifier
   52 |         std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                      ^
processor_support.h:52:72: error: extended character ” is not valid in an identifier
   52 |        std::cerr << “ERROR: please define __cpuid() for this build.\n”;
      |                                                                     ^

In file included from blockwise_sa.h:24,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from blockwise_sa.h:34,
                 from bt2_idx.h:42,
                 from bt2_util.cpp:26:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from blockwise_sa.h:34,
                 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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from bt2_util.cpp:26:
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]
  827 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from bt2_util.cpp:26:
bt2_idx.h:831:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  831 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/memory:83,
                 from bt2_idx.h:28,
                 from bt2_util.cpp:26:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/include/g++-v10/bits/unique_ptr.h:56:28: note: declared here
   56 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from threading.h:26,
                 from ds.h:30,
                 from ref_read.h:33,
                 from reference.h:32,
                 from reference.cpp:22:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from ds.cpp:20:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from multikey_qsort.cpp:20:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from diff_sample.h:24,
                 from multikey_qsort.h:27,
                 from multikey_qsort.cpp:20:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from multikey_qsort.h:27,
                 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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from threading.h:26,
                 from ds.h:30,
                 from random_util.h:25,
                 from random_source.cpp:21:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from diff_sample.h:24,
                 from diff_sample.cpp:20:
/usr/include/tbb/tbb.h:21:154: note: ‘#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from threading.h:26,
                 from ds.h:30,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:31,
                 from diff_sample.cpp:20:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

In file included from diff_sample.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]
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |      ^~
diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  180 |      if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                ^~~~~
diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |      ^~
diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  181 |      if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                ^~~~~
In file included from threading.h:26,
                 from ds.h:30,
                 from bowtie_build_main.cpp:25:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
   21 |  please see Deprecated Features appendix in the TBB reference manual.")
      |                                                                       ^

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-2.2.9:20200513-162919.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'