Bug#925827: shogun: ftbfs with GCC-9
Package: src:shogun
Version: 3.2.0-8
Severity: normal
Tags: sid bullseye
User: debian-gcc@lists.debian.org
Usertags: ftbfs-gcc-9
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/shogun_3.2.0-8_unstable_gcc9.log
The last lines of the build log are at the end of this report.
To build with GCC 9, either set CC=gcc-9 CXX=g++-9 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-9/porting_to.html
GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.
[...]
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/isomap.hpp: In function 'tapkee::DenseSymmetricMatrix tapkee::tapkee_internal::compute_shortest_distances_matrix(const RandomAccessIterator&, const RandomAccessIterator&, const Neighbors&, DistanceCallback) [with RandomAccessIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; DistanceCallback = pimpl_distance_callback<shogun::CDistance>]':
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/isomap.hpp:55:13: error: 'N' not specified in enclosing 'parallel'
55 | bool* f = new bool[N];
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/isomap.hpp:53:9: error: enclosing 'parallel'
53 | #pragma omp parallel shared(shortest_distances,neighbors,begin,callback) default(none)
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/isomap.hpp:106:27: error: 'n_neighbors' not specified in enclosing 'parallel'
106 | for (IndexType i=0; i<n_neighbors; i++)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/isomap.hpp:53:9: error: enclosing 'parallel'
53 | #pragma omp parallel shared(shortest_distances,neighbors,begin,callback) default(none)
| ^~~
In file included from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/methods.hpp:21,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/embed.hpp:11,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/tapkee.hpp:10,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/tapkee_shogun.cpp:23:
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp: In function 'tapkee::DenseSymmetricMatrix tapkee::tapkee_internal::compute_distance_matrix(RandomAccessIterator, RandomAccessIterator, const Landmarks&, PairwiseCallback) [with RandomAccessIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; PairwiseCallback = pimpl_distance_callback<shogun::CDistance>]':
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:43:9: error: 'n_landmarks' not specified in enclosing 'parallel'
43 | #pragma omp for nowait
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:40:9: error: enclosing 'parallel'
40 | #pragma omp parallel shared(begin,landmarks,distance_matrix,callback) default(none)
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp: In function 'tapkee::DenseMatrix tapkee::tapkee_internal::triangulate(RandomAccessIterator, RandomAccessIterator, PairwiseCallback, const Landmarks&, const DenseVector&, tapkee::tapkee_internal::EigendecompositionResult&, tapkee::IndexType) [with RandomAccessIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; PairwiseCallback = pimpl_distance_callback<shogun::CDistance>]':
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:85:15: error: 'n_landmarks' not specified in enclosing 'parallel'
85 | DenseVector distances_to_landmarks(n_landmarks);
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:82:9: error: enclosing 'parallel'
82 | #pragma omp parallel shared(begin,end,to_process,distance_callback,landmarks, \
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:87:9: error: 'n_vectors' not specified in enclosing 'parallel'
87 | #pragma omp for nowait
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:82:9: error: enclosing 'parallel'
82 | #pragma omp parallel shared(begin,end,to_process,distance_callback,landmarks, \
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp: In function 'tapkee::DenseSymmetricMatrix tapkee::tapkee_internal::compute_distance_matrix(RandomAccessIterator, RandomAccessIterator, PairwiseCallback) [with RandomAccessIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; PairwiseCallback = pimpl_distance_callback<shogun::CDistance>]':
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:122:9: error: 'n_vectors' not specified in enclosing 'parallel'
122 | #pragma omp for nowait
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/multidimensional_scaling.hpp:119:9: error: enclosing 'parallel'
119 | #pragma omp parallel shared(begin,distance_matrix,callback) default(none)
| ^~~
In file included from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/methods.hpp:22,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/embed.hpp:11,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/tapkee.hpp:10,
from /<<PKGBUILDDIR>>/src/shogun/lib/tapkee/tapkee_shogun.cpp:23:
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/diffusion_maps.hpp: In function 'tapkee::DenseSymmetricMatrix tapkee::tapkee_internal::compute_diffusion_matrix(RandomAccessIterator, RandomAccessIterator, DistanceCallback, tapkee::IndexType, tapkee::ScalarType) [with RandomAccessIterator = __gnu_cxx::__normal_iterator<int*, std::vector<int> >; DistanceCallback = pimpl_distance_callback<shogun::CDistance>]':
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/diffusion_maps.hpp:51:9: error: 'n_vectors' not specified in enclosing 'parallel'
51 | #pragma omp for nowait
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/diffusion_maps.hpp:48:9: error: enclosing 'parallel'
48 | #pragma omp parallel shared(diffusion_matrix,begin,callback) default(none)
| ^~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/diffusion_maps.hpp:57:32: error: 'width' not specified in enclosing 'parallel'
57 | ScalarType gk = exp(-(k*k)/width);
| ^~~~~
/<<PKGBUILDDIR>>/src/shogun/lib/tapkee/routines/diffusion_maps.hpp:48:9: error: enclosing 'parallel'
48 | #pragma omp parallel shared(diffusion_matrix,begin,callback) default(none)
| ^~~
make[3]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:5378: src/shogun/CMakeFiles/libshogun.dir/lib/tapkee/tapkee_shogun.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[2]: *** [CMakeFiles/Makefile2:194: src/shogun/CMakeFiles/libshogun.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make[1]: *** [Makefile:155: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
dh_auto_build: cd debian/build && make -j1 returned exit code 2
make: *** [debian/rules:13: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
Reply to: