Bug#925779: mlpack: ftbfs with GCC-9

Matthias Klose doko at debian.org
Wed Mar 27 19:47:08 GMT 2019 

Package: src:mlpack
Version: 3.0.4-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at 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/mlpack_3.0.4-1_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.

[...]
make -f src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/build.make src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 27%] Building CXX object src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/det_main.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mlpack/methods/det && /usr/bin/c++  -DARMA_NO_DEBUG -DBOOST_TEST_DYN_LINK -DHAS_OPENMP -DNDEBUG -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mlpack/..  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -ftemplate-depth=1000 -O3 -fopenmp   -DBINDING_TYPE=BINDING_TYPE_CLI -std=gnu++11 -o CMakeFiles/mlpack_det.dir/det_main.cpp.o -c /<<PKGBUILDDIR>>/src/mlpack/methods/det/det_main.cpp
In file included from /<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils.hpp:147,
                 from /<<PKGBUILDDIR>>/src/mlpack/methods/det/det_main.cpp:15:
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp: In function 'mlpack::det::DTree<MatType, TagType>* mlpack::det::Trainer(MatType&, size_t, bool, size_t, size_t, bool) [with MatType = arma::Mat<double>; TagType = int]':
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:189:3: error: 'folds' not specified in enclosing 'parallel'
  189 |   for (omp_size_t fold = 0; fold < (omp_size_t) folds; fold++)
      |   ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:192:33: error: 'testSize' not specified in enclosing 'parallel'
  192 |     const size_t start = fold * testSize;
      |                                 ^~~~~~~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:194:61: error: 'cvData' not specified in enclosing 'parallel'
  194 |                                 * testSize, (size_t) cvData.n_cols);
      |                                                      ~~~~~~~^~~~~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:222:5: error: 'minLeafSize' not specified in enclosing 'parallel'
  222 |     cvDTree.Grow(train, cvOldFromNew, useVolumeReg, maxLeafSize,
      |     ^~~~~~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:222:5: error: 'maxLeafSize' not specified in enclosing 'parallel'
  222 |     cvDTree.Grow(train, cvOldFromNew, useVolumeReg, maxLeafSize,
      |     ^~~~~~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:222:5: error: 'useVolumeReg' not specified in enclosing 'parallel'
  222 |     cvDTree.Grow(train, cvOldFromNew, useVolumeReg, maxLeafSize,
      |     ^~~~~~~
/<<PKGBUILDDIR>>/src/mlpack/methods/det/dt_utils_impl.hpp:187:11: error: enclosing 'parallel'
  187 |   #pragma omp parallel for default(none) \
      |           ^~~
make[4]: *** [src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/build.make:66: src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/det_main.cpp.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:2300: src/mlpack/methods/det/CMakeFiles/mlpack_det.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 27%] Linking CXX executable ../../../../bin/mlpack_decision_stump
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mlpack/methods/decision_stump && /usr/bin/cmake -E cmake_link_script CMakeFiles/mlpack_decision_stump.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -ftemplate-depth=1000 -O3 -fopenmp  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mlpack_decision_stump.dir/decision_stump_main.cpp.o  -o ../../../../bin/mlpack_decision_stump -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib: ../../../../lib/libmlpack.so.3.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so -lpthread /usr/lib/libarmadillo.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 27%] Built target mlpack_decision_stump
[ 28%] Linking CXX executable ../../../../bin/mlpack_decision_tree
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mlpack/methods/decision_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/mlpack_decision_tree.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -ftemplate-depth=1000 -O3 -fopenmp  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mlpack_decision_tree.dir/decision_tree_main.cpp.o  -o ../../../../bin/mlpack_decision_tree -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib: ../../../../lib/libmlpack.so.3.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so -lpthread /usr/lib/libarmadillo.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 28%] Built target mlpack_decision_tree
[ 28%] Linking CXX executable ../../../../bin/mlpack_dbscan
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/mlpack/methods/dbscan && /usr/bin/cmake -E cmake_link_script CMakeFiles/mlpack_dbscan.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -ftemplate-depth=1000 -O3 -fopenmp  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/mlpack_dbscan.dir/dbscan_main.cpp.o  -o ../../../../bin/mlpack_dbscan -Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib: ../../../../lib/libmlpack.so.3.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so -lpthread /usr/lib/libarmadillo.so /usr/lib/x86_64-linux-gnu/libboost_program_options.so /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 28%] Built target mlpack_dbscan
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:144: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:56: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:44: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2

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