make[1]: Entering directory '/<<PKGBUILDDIR>>'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-
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 --
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
fixed 1060971 1.9.9-1Bug #1060971 [src:mdtraj] mdtraj: FTBFS: dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
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