Bug#925668: deal.ii: ftbfs with GCC-9

[Matthias Klose]

Package: src:deal.ii
Version: 9.0.1-1
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/deal.ii_9.0.1-1_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.

[...]
  *** abort




11% tests passed, 17 tests failed out of 19

Total Test time (real) = 212.00 sec

The following tests FAILED:
	  1 - step.debug (Failed)
	  3 - affinity.debug (Failed)
	  4 - mpi.debug (Failed)
	  5 - tbb.debug (Failed)
	  6 - p4est.debug (Failed)
	  7 - step-petsc.debug (Failed)
	  8 - step-slepc.debug (Failed)
	  9 - step-trilinos.debug (Failed)
	 10 - lapack.debug (Failed)
	 11 - umfpack.debug (Failed)
	 12 - gsl.debug (Failed)
	 14 - arpack.debug (Failed)
	 15 - sundials-ida.debug (Failed)
	 16 - assimp.debug (Failed)
	 17 - scalapack.debug (Failed)
	 18 - boost_zlib.debug (Failed)
	 19 - gmsh.debug (Failed)
Errors while running CTest

***************************************************************************
**                 Error: Some of the quick tests failed.                **
***************************************************************************

Please scroll up or check the file tests/quick_tests/quicktests.log for the
error messages. If you are unable to fix the problems, see the FAQ or write
to the mailing list linked at http://www.dealii.org


The affinity test can fail when you are linking in a library like BLAS
which uses OpenMP. Even without calling any BLAS functions, OpenMP messes
with the thread affinity which causes TBB to run single-threaded only. You
can fix this by exporting OMP_NUM_THREADS=1. Also see GOMP_CPU_AFFINITY 
and OMP_PROC_BIND.


The p4est test can fail if you are running an OpenMPI version before 1.5.
This is a known problem and the only work around is to update to a more
recent version or use a different MPI library like MPICH.


Additional information about PETSc issues is available
at:
http://www.dealii.org/developer/external-libs/petsc.html

CMake Error at /<<PKGBUILDDIR>>/tests/quick_tests/run.cmake:68 (MESSAGE):


make[5]: *** [tests/quick_tests/CMakeFiles/test.dir/build.make:61: tests/quick_tests/CMakeFiles/test] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:10612: tests/quick_tests/CMakeFiles/test.dir/all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:10619: tests/quick_tests/CMakeFiles/test.dir/rule] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:3508: test] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_test: cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=-j1 returned exit code 2
make[1]: *** [debian/rules:50: override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2