Source: mdtraj
Version: 1.9.7-6
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240115 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<>'
> dh_auto_clean || /bin/true
> I: pybuild base:305: python3.12 setup.py clean
> Using built-in specs.
> COLLECT_GCC=/usr/bin/x86_64-linux-gnu-gcc
> COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper
> OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
> OFFLOAD_TARGET_DEFAULT=1
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Debian 13.2.0-9'
> --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs
> --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr
> --with-gcc-major-version-only --program-suffix=-13
> --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id
> --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix
> --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu
> --enable-libstdcxx-debug --enable-libstdcxx-time=yes
> --with-default-libstdcxx-abi=new --enable-gnu-unique-object
> --disable-vtable-verify --enable-plugin --enable-default-pie
> --with-system-zlib --enable-libphobos-checking=release
> --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch
> --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64
> --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic
> --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-13-13.2.0/debian/tmp-gcn/usr
> --enable-offload-defaulted --without-cuda-driver --enable-checking=release
> --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
> Thread model: posix
> Supported LTO compression algorithms: zlib zstd
> gcc version 13.2.0 (Debian 13.2.0-9)
> /<>/basesetup.py:431: UserWarning: Unrecognized setuptools
> command ('clean'), proceeding with generating Cython sources and expanding
> templates
> warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
> warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in
> shared declaration (e.g. mix of pointers and values). Each pointer
> declaration should be on its own line.
> warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in
> shared declaration (e.g. mix of pointers and values). Each pointer
> declaration should be on its own line.
> warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in
> shared declaration (e.g. mix of pointers and values). Each pointer
> declaration should be on its own line.
> performance hint: mdtraj/geometry/src/image_molecules.pxi:13:5: Exception
> check on 'make_whole' will always require the GIL to be acquired.
> Possible solutions:
> 1. Declare 'make_whole' as 'noexcept' if you control the definition and
> you're sure you don't want the function to raise exceptions.
> 2. Use an 'int' return type on 'make_whole' to allow an error code to
> be returned.
>
> Error compiling Cython file:
>
> ...
> offset[k] += frame_unitcell_vectors[0,
> k]*roundf((delta[0]-offset[0])/frame_unitcell_vectors[0,0])
> frame_positions[atom2, k] = frame_positions[atom2, k] - offset[k]
>
> cdef void anchor_dists(float[:,::1] frame_positions,
> float[:,::1] frame_unitcell_vectors,
> vector[int[:]] anchor_molecules,
> ^
>
>
> mdtraj/geometry/src/image_molecules.pxi:33:24: Reference-counted type
> 'int[:]' cannot be used as a template argument
> performance hint: mdtraj/geometry/src/image_molecules.pxi:31:5: Exception
> check on 'anchor_dists' will always require the GIL to be acquired.
> Possible solutions:
> 1. Declare 'anchor_dists' as 'noexcept' if you control the definition
> and you're sure you don't want the function to raise exceptions.
> 2. Use an 'int' return type on 'anchor_dists' to allow an error code to
> be returned.
>
> Error compiling Cython file:
>
> ...
> anchor_nearest_atoms[mol2, mol1, 1] = ca2
>
> cdef void wrap_mols(float[:,::1] frame_positions,
> float[:,::1] frame_unitcell_vectors,
> float[:] center,
> vector[int[:]] other_molecules) nogil:
> ^
>
>
> mdtraj/geometry/src/image_molecules.pxi:55:26: Reference-counted type
> 'int[:]' cannot be used as a template argument
> performance
