[Debichem-devel] Bug#1045994: mdtraj: Fails to build source after successful build

Sun Aug 13 20:20:58 BST 2023

Source: mdtraj
Version: 1.9.7-6
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> -------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package mdtraj
> dpkg-buildpackage: info: source version 1.9.7-6
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Drew Parsons <dparsons at debian.org>
>  dpkg-source --before-build .
> dpkg-source: info: using options from mdtraj-1.9.7/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/
>  fakeroot debian/rules clean
> dh clean --with python3,sphinxdoc --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean || /bin/true
> I: pybuild base:275: python3.11 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 13.2.0-2' --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 13.2.0-2) 
> /<<PKGBUILDDIR>>/basesetup.py:431: UserWarning: Unrecognized setuptools command ('clean'), proceeding with generating Cython sources and expanding templates
>   warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
>   if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
>   obj = getattr(themodule, elem)
> 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.
> 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/dcd/dcd.pyx
> [ 2/12] Cythonizing mdtraj/geometry/drid.pyx
> [ 3/12] Cythonizing mdtraj/geometry/neighborlist.pyx
> [ 4/12] Cythonizing mdtraj/geometry/neighbors.pyx
> [ 5/12] Cythonizing mdtraj/geometry/src/_geometry.pyx
> [ 6/12] Cythonizing mdtraj/rmsd/_lprmsd.pyx
> [ 7/12] Cythonizing mdtraj/formats/binpos/binpos.pyx
> [ 8/12] Cythonizing mdtraj/formats/dtr/dtr.pyx
> [ 9/12] Cythonizing mdtraj/formats/tng/tng.pyx
> [10/12] Cythonizing mdtraj/formats/xtc/trr.pyx
> [11/12] Cythonizing mdtraj/formats/xtc/xtc.pyx
> [12/12] Cythonizing mdtraj/rmsd/_rmsd.pyx
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_mdtraj/build' (and everything under it)
> 'build/bdist.linux-x86_64' does not exist -- can't clean it
> 'build/scripts-3.11' does not exist -- can't clean it
> 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: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.Topology.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.Trajectory.superpose.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.acylindricity.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.asphericity.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.baker_hubbard.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_ppm.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_shiftx2.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.chemical_shifts_spartaplus.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_C.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_CB.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_J3_HN_HA.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_angles.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_center_of_mass.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_chi1.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_chi2.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_chi3.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_chi4.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_contacts.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_dihedrals.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_directors.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_displacements.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_distances.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_drid.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_dssp.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_gyration_tensor.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_inertia_tensor.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_neighbors.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_nematic_order.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_omega.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_phi.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_psi.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_rdf.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.compute_rg.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.density.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.dipole_moments.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.AmberNetCDFRestartFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.AmberRestartFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.ArcTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.BINPOSTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.DCDTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.DTRTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.GroTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.HDF5TrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.LAMMPSTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.LH5TrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.MDCRDTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.NetCDFTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.PDBTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.TRRTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.XTCTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.formats.XYZTrajectoryFile.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.geometry.squareform.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.isothermal_compressability_kappa_T.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.iterload.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.join.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.kabsch_sander.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_arc.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_binpos.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_dcd.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_dtr.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_frame.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_hdf5.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_hoomdxml.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_lammpstrj.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_lh5.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_netcdf.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_pdb.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_prmtop.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_trr.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_xml.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_xtc.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.load_xyz.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.lprmsd.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.open.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.principal_moments.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.reindex_dataframe_by_atoms.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.relative_shape_antisotropy.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.reporters.DCDReporter.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.reporters.HDF5Reporter.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.reporters.NetCDFReporter.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.rmsd.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.rmsf.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.shrake_rupley.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.static_dielectric.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.thermal_expansion_alpha_P.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.box_vectors_to_lengths_and_angles.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.check_random_state.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ensure_type.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.ilen.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.import_.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.in_units_of.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.lengths_and_angles_to_box_vectors.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.rotation_matrix_from_quaternion.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.timing.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.utils.uniform_quaternion.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/docs/api/generated/mdtraj.wernet_nilsson.rst has no final newline (either original or modified version)
> dpkg-source: warning: file mdtraj-1.9.7/mdtraj/core/lib/center.h has no final newline (either original or modified version)
> dpkg-source: error: cannot represent change to mdtraj/core/lib/libtheobald.a: binary file contents changed
> dpkg-source: error: add mdtraj/core/lib/libtheobald.a in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.

The full build log is available from:
http://qa-logs.debian.net/2023/08/13/mdtraj_1.9.7-6_unstable.log

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.