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 '/<<PKGBUILDDIR>>'
> 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)
> /<<PKGBUILDDIR>>/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 hint: mdtraj/geometry/src/image_molecules.pxi:52:5: Exception
> check on 'wrap_mols' will always require the GIL to be acquired.
> Possible solutions:
> 1. Declare 'wrap_mols' 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 'wrap_mols' to allow an error code to be
> returned.
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
>
>
> cdef void image_frame(frame_positions,
> frame_unitcell_vectors,
> anchor_molecules,
> vector[int[:]] other_molecules,
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:96:23: Reference-counted type
> 'int[:]' cannot be used as a template argument
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
> anchor_atom_indices = np.concatenate(anchor_molecules)
> center = np.mean(frame_positions[anchor_atom_indices], axis=0)
> wrap_mols(frame_positions, frame_unitcell_vectors, center,
> other_molecules)
>
> def image_molecules(xyz, box, anchor_molecules, other_molecules,
> sorted_bonds):
> cdef vector[int[:]] omol = other_molecules
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:144:15: Reference-counted type
> 'int[:]' cannot be used as a template argument
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
> cdef int[:] mol
> cdef float mol_center[3]
> cdef float mol_offset[3]
>
> cdef int n
> for i in range(other_molecules.size()):
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:72:39: Coercion from Python not
> allowed without the GIL
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
> cdef int[:] mol
> cdef float mol_center[3]
> cdef float mol_offset[3]
>
> cdef int n
> for i in range(other_molecules.size()):
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:72:39: Calling gil-requiring function
> not allowed without gil
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
> cdef int[:] mol
> cdef float mol_center[3]
> cdef float mol_offset[3]
>
> cdef int n
> for i in range(other_molecules.size()):
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:72:34: Accessing Python attribute not
> allowed without gil
>
> Error compiling Cython file:
> ------------------------------------------------------------
> ...
> cdef int[:] mol
> cdef float mol_center[3]
> cdef float mol_offset[3]
>
> cdef int n
> for i in range(other_molecules.size()):
> ^
> ------------------------------------------------------------
>
> mdtraj/geometry/src/image_molecules.pxi:72:39: Constructing Python tuple not
> allowed without gil
> C compiler:
> Attempting to autodetect OpenMP support... Compiler supports OpenMP
> Attempting to autodetect SSE3 support... Compiler supports SSE3
> Attempting to autodetect SSE4.1 support... Compiler supports SSE4.1
> Attempting to autodetect NEON support... Did not detect NEON support
>
> [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
> [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx
> [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
> [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx
> [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx
> [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
> [ 7/12] Cythonizing mdtraj/geometry/drid.pyx
> [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx
> [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx
> [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/setup.py", line 301, in <module>
> metadata['ext_modules'] = cythonize(
> ^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line
> 1154, in cythonize
> cythonize_one(*args)
> File "/usr/lib/python3/dist-packages/Cython/Build/Dependencies.py", line
> 1321, in cythonize_one
> raise CompileError(None, pyx_file)
> Cython.Compiler.Errors.CompileError: mdtraj/geometry/src/_geometry.pyx
> E: pybuild pybuild:391: clean: plugin distutils failed with: exit code=1:
> python3.12 setup.py clean
> dh_auto_clean: error: pybuild --clean -i python{version} -p "3.12 3.11"
> returned exit code 13
> for f in mdtraj/formats/binpos/binpos.c \
> mdtraj/formats/dcd/dcd.c \
> mdtraj/formats/dtr/dtr.cpp \
> mdtraj/formats/tng/tng.c \
> mdtraj/formats/xtc/trr.c \
> mdtraj/formats/xtc/xtc.c \
> mdtraj/geometry/drid.cpp \
> mdtraj/geometry/neighborlist.cpp \
> mdtraj/geometry/neighbors.cpp \
> mdtraj/geometry/src/_geometry.cpp \
> mdtraj/rmsd/_lprmsd.cpp \
> mdtraj/rmsd/_rmsd.cpp \
> mdtraj/version.py; \
> do rm -f $f; done
> rm -rf __pycache__
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean -O--buildsystem=pybuild
> dh_clean -O--buildsystem=pybuild
> dpkg-source -b .
> dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options:
> --extend-diff-ignore=^[^/]*[.]egg-info/
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building mdtraj using existing ./mdtraj_1.9.7.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: info: local changes detected, the modified files are:
> mdtraj-1.9.7/.pybuild/cpython3_3.12_mdtraj/.pydistutils.cfg
> dpkg-source: error: aborting due to unexpected upstream changes, see
> /tmp/mdtraj_1.9.7-6.diff.4gSP2o
> dpkg-source: info: Hint: make sure the version in debian/changelog matches
> the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source
> --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> --------------------------------------------------------------------------------
> Build finished at 2024-01-15T20:15:36Z
The full build log is available from:
http://qa-logs.debian.net/2024/01/15/mdtraj_1.9.7-6_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240115;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240115&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
