Source: adios
Version: 1.13.1-16
Severity: serious
Tags: buster sid
User: [email protected]
Usertags: qa-ftbfs-20190315 qa-ftbfs
Justification: FTBFS in buster on amd64
Hi,
During a rebuild of all packages in buster (in a buster chroot, not a
sid chroot), your package failed to build on amd64.
Relevant part (hopefully):
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
> -fdebug-prefix-map=/build/python2.7-UboFgi/python2.7-2.7.16~rc1=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
> build/temp.linux-x86_64-2.7/adios.o -L../../debian/tmp/usr/lib
> -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/sr/lib
> -ladios_nompi -libverbs -lnetcdf -lhdf5_hl -lhdf5 -lz -lglib-2.0 -lz -lbz2
> -lsz -llz4 -lblosc -lm -lpthread -lrt -o
> build/lib.linux-x86_64-2.7/adios/adios.so
> python setup_mpi.py build
> running build
> running build_src
> running build_py
> creating build/lib.linux-x86_64-2.7/adios_mpi
> copying src_mpi/__init__.py -> build/lib.linux-x86_64-2.7/adios_mpi
> creating build/lib.linux-x86_64-2.7/adios_mpi/_hl
> copying _hl/selections.py -> build/lib.linux-x86_64-2.7/adios_mpi/_hl
> copying _hl/__init__.py -> build/lib.linux-x86_64-2.7/adios_mpi/_hl
> running build_ext
> MPI configuration: [mpi] from 'mpi.cfg'
> MPI C compiler: /usr/bin/mpicc
> MPI C++ compiler: /usr/bin/mpicxx
> MPI F77 compiler: /usr/bin/mpif77
> MPI F90 compiler: /usr/bin/mpif90
> building 'adios_mpi.adios_mpi' extension
> /usr/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -I/usr/lib/python2.7/dist-packages/numpy/core/include
> -I../../src/public -I/usr/include
> -I/usr/lib/x86_64-linux-gnu/netcdf/mpi/include -I/usr/include/hdf5/openmpi
> -I/usr/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
> -I/usr/include -I/usr/include -I/usr/include -I/sr/include -I/usr/include
> -I/sr/include -I/usr/include -I/usr/include/python2.7 -c adios_mpi.cpp -o
> build/temp.linux-x86_64-2.7/adios_mpi.o -Wno-unused-function
> -Wno-uninitialized
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid for
> C/ObjC but not for C++
> In file included from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
> from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
> from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
> from adios_mpi.cpp:629:
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
> warning: #warning "Using deprecated NumPy API, disable it with " "#define
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> #warning "Using deprecated NumPy API, disable it with " \
> ^~~~~~~
> /usr/bin/mpicxx -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro
> -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
> -Wdate-time -D_FORTIFY_SOURCE=2 -g
> -fdebug-prefix-map=/build/python2.7-UboFgi/python2.7-2.7.16~rc1=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wl,-z,relro build/temp.linux-x86_64-2.7/adios_mpi.o
> -L../../debian/tmp/usr/lib -L/usr/lib/x86_64-linux-gnu
> -L/usr/lib/x86_64-linux-gnu/netcdf/mpi
> -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -L/sr/lib -ladios -lnetcdf -lhdf5_hl
> -lhdf5 -lz -libverbs -lglib-2.0 -lz -lbz2 -lsz -llz4 -lblosc -lm -lpthread -o
> build/lib.linux-x86_64-2.7/adios_mpi/adios_mpi.so
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/wrappers/numpy'
> # MPICH
> install -D -t debian/tmp/usr/lib build-mpich/src/*.a
> for p in python2.7 python3.7 ; do \
> ( cd build-mpich/numpy && \
> $p ./setup_mpi.py build_ext --mpicc=mpicc.mpich --mpicxx=mpicxx.mpich )
> ; \
> done
> running build_ext
> MPI configuration: [mpi] from 'mpi.cfg'
> MPI C compiler: /usr/bin/mpicc.mpich
> MPI C++ compiler: /usr/bin/mpicxx.mpich
> building 'adios_mpi.adios_mpi' extension
> creating build
> creating build/temp.linux-x86_64-2.7
> /usr/bin/mpicc.mpich -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -I/usr/lib/python2.7/dist-packages/numpy/core/include
> -I../../src/public -I/usr/include
> -I/usr/lib/x86_64-linux-gnu/netcdf/mpi/include -I/usr/include/hdf5/openmpi
> -I/usr/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
> -I/usr/include -I/usr/include -I/usr/include -I/sr/include -I/usr/include
> -I/sr/include -I/usr/include -I/usr/include/python2.7 -c adios_mpi.cpp -o
> build/temp.linux-x86_64-2.7/adios_mpi.o -Wno-unused-function
> -Wno-uninitialized
> cc1plus: warning: command line option '-Wstrict-prototypes' is valid for
> C/ObjC but not for C++
> In file included from /usr/include/x86_64-linux-gnu/mpich/mpi.h:2241,
> from mpi-compat.h:7,
> from adios_mpi.cpp:537:
> /usr/include/x86_64-linux-gnu/mpich/mpicxx.h:22:4: error: #error 'Please use
> the same version of GCC and g++ for compiling MPICH and user MPI programs'
> # error 'Please use the same version of GCC and g++ for compiling MPICH and
> user MPI programs'
> ^~~~~
> In file included from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
> from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
> from
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
> from adios_mpi.cpp:541:
> /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
> warning: #warning "Using deprecated NumPy API, disable it with " "#define
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> #warning "Using deprecated NumPy API, disable it with " \
> ^~~~~~~
> Traceback (most recent call last):
> File "./setup_mpi.py", line 148, in <module>
> package_dir = {'adios_mpi': 'src_mpi', 'adios_mpi._hl': '_hl'},
> File "/<<PKGBUILDDIR>>/build-mpich/numpy/conf/mpidistutils.py", line 494,
> in setup
> return fcn_setup(**attrs)
> File "/usr/lib/python2.7/distutils/core.py", line 151, in setup
> dist.run_commands()
> File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
> self.run_command(cmd)
> File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
> cmd_obj.run()
> File "/<<PKGBUILDDIR>>/build-mpich/numpy/conf/mpidistutils.py", line 1077,
> in run
> cmd_build_ext.build_ext.run(self)
> File "/usr/lib/python2.7/distutils/command/build_ext.py", line 340, in run
> self.build_extensions()
> File "/<<PKGBUILDDIR>>/build-mpich/numpy/conf/mpidistutils.py", line 1106,
> in build_extensions
> if not ext.optional: raise
> AttributeError: Extension instance has no attribute 'optional'
> running build_ext
> MPI configuration: [mpi] from 'mpi.cfg'
> MPI C compiler: /usr/bin/mpicc.mpich
> MPI C++ compiler: /usr/bin/mpicxx.mpich
> building 'adios_mpi.adios_mpi' extension
> creating build/temp.linux-x86_64-3.7
> /usr/bin/mpicc.mpich -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g
> -fwrapv -O2 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -I/usr/lib/python3/dist-packages/numpy/core/include
> -I../../src/public -I/usr/include
> -I/usr/lib/x86_64-linux-gnu/netcdf/mpi/include -I/usr/include/hdf5/openmpi
> -I/usr/include -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
> -I/usr/include -I/usr/include -I/usr/include -I/sr/include -I/usr/include
> -I/sr/include -I/usr/include -I/usr/include/python3.7m -c adios_mpi.cpp -o
> build/temp.linux-x86_64-3.7/adios_mpi.o -Wno-unused-function
> -Wno-uninitialized
> In file included from /usr/include/x86_64-linux-gnu/mpich/mpi.h:2241,
> from mpi-compat.h:7,
> from adios_mpi.cpp:537:
> /usr/include/x86_64-linux-gnu/mpich/mpicxx.h:22:4: error: #error 'Please use
> the same version of GCC and g++ for compiling MPICH and user MPI programs'
> # error 'Please use the same version of GCC and g++ for compiling MPICH and
> user MPI programs'
> ^~~~~
> In file included from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
> from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
> from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
> from adios_mpi.cpp:541:
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
> warning: #warning "Using deprecated NumPy API, disable it with " "#define
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> #warning "Using deprecated NumPy API, disable it with " \
> ^~~~~~~
> error: command '/usr/bin/mpicc.mpich' failed with exit status 1
> make[1]: *** [debian/rules:123: override_dh_auto_build] Error 1
The full build log is available from:
http://aws-logs.debian.net/2019/03/15/adios_1.13.1-16_testing.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
