sci-biology:amap-2.2-r5:20231208-181014.log

sci-biology:amap-2.2-r5:20231208-181014.log (text/plain), 10.25 KB, created by Toralf Förster on 2023-12-08 18:35:03 UTC

 * Package:    sci-biology/amap-2.2-r5:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc java kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking amap.2.2.tar.gz to /var/tmp/portage/sci-biology/amap-2.2-r5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/amap-2.2-r5/work
>>> Preparing source in /var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align ...
 * Applying amap-2.2-makefile.patch ...
 [ ok ]
 * Applying amap-2.2-includes.patch ...
 [ ok ]
>>> Source prepared.
 * Modern C testing: this build is using a /etc/portage/bashrc hook (2023-11-30T22:24)!
 * Modern C testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info.
>>> Configuring source in /var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align ...
make -j4 -C align 
make: Entering directory '/var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align/align'
clang++ -Wl,-O1 -Wl,--as-needed -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -O2 -pipe -march=native -fno-diagnostics-color -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -o amap Amap.cc -lm
In file included from Amap.cc:7:
./SafeVector.h:29:3: warning: definition of implicit copy assignment operator
      for 'SafeVector<char>' is deprecated because it has a user-provided copy
      constructor [-Wdeprecated-copy-with-user-provided-copy]
   29 |   SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
      |   ^
./Sequence.h:293:18: note: in implicit copy assignment operator for
      'SafeVector<char>' first required here
  293 |     *(ret->data) = *data;
      |                  ^
In file included from Amap.cc:9:
./MultiSequenceDag.h:329:23: error: no template named 'binary_function'; did you
      mean '__binary_function'?
  329 | class greater_index : binary_function<Column*, Column*, bool> {
      |                       ^~~~~~~~~~~~~~~
      |                       __binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: 
      '__binary_function' declared here
   49 | using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg...
      | ^
In file included from Amap.cc:9:
./MultiSequenceDag.h:341:23: error: no template named 'binary_function'; did you
      mean '__binary_function'?
  341 | class smaller_index : binary_function<Column*, Column*, bool> {
      |                       ^~~~~~~~~~~~~~~
      |                       __binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: 
      '__binary_function' declared here
   49 | using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg...
      | ^
In file included from Amap.cc:9:
./MultiSequenceDag.h:353:24: error: no template named 'binary_function'; did you
      mean '__binary_function'?
  353 | class smaller_weight : binary_function<Edge*, Edge*, bool> {
      |                        ^~~~~~~~~~~~~~~
      |                        __binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: 
      '__binary_function' declared here
   49 | using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg...
      | ^
In file included from Amap.cc:9:
./MultiSequenceDag.h:749:92: warning: '&&' within '||'
      [-Wlogical-op-parentheses]
  749 |   ...|| consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) 
      |      ~~ ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./MultiSequenceDag.h:749:92: note: place parentheses around the '&&' expression
      to silence this warning
  749 |   ...consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) 
      |                       ^                                                                  
      |      (                                                                                   )
In file included from Amap.cc:12:
./ProbabilisticModel.h:504:31: warning: '&&' within '||'
      [-Wlogical-op-parentheses]
  504 |             if (enableTrainEmissions && i != 1 || j != 1){
      |                 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ ~~
./ProbabilisticModel.h:504:31: note: place parentheses around the '&&'
      expression to silence this warning
  504 |             if (enableTrainEmissions && i != 1 || j != 1){
      |                                      ^
      |                 (                             )
In file included from Amap.cc:7:
./SafeVector.h:29:3: warning: definition of implicit copy assignment operator
      for 'SafeVector<SafeVector<SparseMatrix *>>' is deprecated because it has
      a user-provided copy constructor
      [-Wdeprecated-copy-with-user-provided-copy]
   29 |   SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
      |   ^
Amap.cc:482:22: note: in implicit copy assignment operator for
      'SafeVector<SafeVector<SparseMatrix *>>' first required here
  482 |       sparseMatrices = originalSparseMatrices;
      |                      ^
In file included from Amap.cc:7:
./SafeVector.h:29:3: warning: definition of implicit copy assignment operator
      for 'SafeVector<SafeVector<float>>' is deprecated because it has a
      user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
   29 |   SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
      |   ^
Amap.cc:1075:13: note: in implicit copy assignment operator for
      'SafeVector<SafeVector<float>>' first required here
 1075 |   emitPairs = VVF (256, VF (256, 1e-10));
      |             ^
In file included from Amap.cc:7:
./SafeVector.h:29:3: warning: definition of implicit copy assignment operator
      for 'SafeVector<float>' is deprecated because it has a user-provided copy
      constructor [-Wdeprecated-copy-with-user-provided-copy]
   29 |   SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
      |   ^
Amap.cc:1076:14: note: in implicit copy assignment operator for
      'SafeVector<float>' first required here
 1076 |   emitSingle = VF (256, 1e-5);
      |              ^
In file included from Amap.cc:7:
./SafeVector.h:29:3: warning: definition of implicit copy assignment operator
      for 'SafeVector<SparseMatrix *>' is deprecated because it has a
      user-provided copy constructor [-Wdeprecated-copy-with-user-provided-copy]
   29 |   SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
      |   ^
/usr/include/c++/v1/__algorithm/copy.h:40:17: note: in implicit copy assignment
      operator for 'SafeVector<SparseMatrix *>' first required here
   40 |       *__result = *__first;
      |                 ^
/usr/include/c++/v1/__algorithm/copy_move_common.h:109:19: note: in
      instantiation of function template specialization
      'std::__copy_loop<std::_ClassicAlgPolicy>::operator()<SafeVector<SparseMatrix
      *> *, SafeVector<SparseMatrix *> *, SafeVector<SparseMatrix *> *>'
      requested here
  109 |   auto __result = _Algorithm()(std::move(__range.first), std::move(__ran...
      |                   ^
/usr/include/c++/v1/__algorithm/copy_move_common.h:133:15: note: in
      instantiation of function template specialization
      'std::__unwrap_and_dispatch<std::__overload<std::__copy_loop<std::_ClassicAlgPolicy>,
      std::__copy_trivial>, SafeVector<SparseMatrix *> *,
      SafeVector<SparseMatrix *> *, SafeVector<SparseMatrix *> *, 0>' requested
      here
  133 |   return std::__unwrap_and_dispatch<_Algorithm>(std::move(__first), std:...
      |               ^
/usr/include/c++/v1/__algorithm/copy.h:110:15: note: in instantiation of
      function template specialization
      'std::__dispatch_copy_or_move<std::_ClassicAlgPolicy,
      std::__copy_loop<std::_ClassicAlgPolicy>, std::__copy_trivial,
      SafeVector<SparseMatrix *> *, SafeVector<SparseMatrix *> *,
      SafeVector<SparseMatrix *> *>' requested here
  110 |   return std::__dispatch_copy_or_move<_AlgPolicy, __copy_loop<_AlgPolicy...
      |               ^
/usr/include/c++/v1/vector:1461:32: note: in instantiation of function template
      specialization 'std::__copy<std::_ClassicAlgPolicy,
      SafeVector<SparseMatrix *> *, SafeVector<SparseMatrix *> *,
      SafeVector<SparseMatrix *> *>' requested here
 1461 |             pointer __m = std::__copy<_ClassicAlgPolicy>(__first, __last...
      |                                ^
/usr/include/c++/v1/vector:1443:3: note: in instantiation of function template
      specialization 'std::vector<SafeVector<SparseMatrix
      *>>::__assign_with_size<SafeVector<SparseMatrix *> *,
      SafeVector<SparseMatrix *> *>' requested here
 1443 |   __assign_with_size(__first, __last, std::distance(__first, __last));
      |   ^
/usr/include/c++/v1/vector:1412:9: note: in instantiation of function template
      specialization 'std::vector<SafeVector<SparseMatrix
      *>>::assign<SafeVector<SparseMatrix *> *, 0>' requested here
 1412 |         assign(__x.__begin_, __x.__end_);
      |         ^
./SafeVector.h:22:7: note: in instantiation of member function
      'std::vector<SafeVector<SparseMatrix *>>::operator=' requested here
   22 | class SafeVector : public std::vector<TYPE>{
      |       ^
7 warnings and 3 errors generated.
make: *** [Makefile:40: amap] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align/align'
 * ERROR: sci-biology/amap-2.2-r5::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/amap-2.2-r5::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/amap-2.2-r5::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:amap-2.2-r5:20231208-181014.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/amap-2.2-r5/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/amap-2.2-r5/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align'
 * S: '/var/tmp/portage/sci-biology/amap-2.2-r5/work/amap-align'
!!! When you file a bug report, please include the following information:
GENTOO_VM=  CLASSPATH="" JAVA_HOME=""
JAVACFLAGS="" COMPILER=""
and of course, the output of emerge --info =amap-2.2