Bug#1049827: lammps: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 09:26:37 BST 2023
Source: lammps
Version: 20220106.git7586adbb6a+ds1-2
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
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/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ----------------------------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package lammps
> dpkg-buildpackage: info: source version 20220106.git7586adbb6a+ds1-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Anton Gladky <gladk at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> fakeroot debian/rules clean
> dh clean --with python3 --with-sphinxdoc --sourcedirectory=cmake --builddirectory=/<<PKGBUILDDIR>>/debian/build
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> rm -rf /<<PKGBUILDDIR>>/debian/build
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean -O--with-sphinxdoc -O--sourcedirectory=cmake -O--builddirectory=/<<BUILDDIR>>/lammps-20220106.git7586adbb6a\+ds1/debian/build
> dh_clean -O--with-sphinxdoc -O--sourcedirectory=cmake -O--builddirectory=/<<BUILDDIR>>/lammps-20220106.git7586adbb6a\+ds1/debian/build
> debian/rules build
> dh build --with python3 --with-sphinxdoc --sourcedirectory=cmake --builddirectory=/<<PKGBUILDDIR>>/debian/build
> dh_update_autotools_config -O--with-sphinxdoc -O--sourcedirectory=cmake -O--builddirectory=/<<BUILDDIR>>/lammps-20220106.git7586adbb6a\+ds1/debian/build
> dh_autoreconf -O--with-sphinxdoc -O--sourcedirectory=cmake -O--builddirectory=/<<BUILDDIR>>/lammps-20220106.git7586adbb6a\+ds1/debian/build
> debian/rules override_dh_auto_configure
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_configure -- \
> -DBUILD_SHARED_LIBS=ON \
> -DCMAKE_SKIP_INSTALL_RPATH=TRUE \
> -DPKG_ASPHERE=ON \
> -DPKG_BODY=ON \
> -DPKG_CLASS2=ON \
> -DPKG_COLLOID=ON \
> -DPKG_COMPRESS=ON \
> -DPKG_CORESHELL=ON \
> -DPKG_EXTRA-PAIR=ON \
> -DPKG_DIPOLE=ON \
> -DPKG_GPU=OFF \
> -DPKG_GRANULAR=ON \
> -DPKG_KIM=ON \
> -DPKG_KSPACE=ON \
> -DPKG_MANYBODY=ON \
> -DPKG_MC=ON \
> -DPKG_MISC=ON \
> -DPKG_MOLECULE=ON \
> -DPKG_MPIIO=ON \
> -DPKG_OPT=ON \
> -DPKG_PERI=ON \
> -DPKG_POEMS=ON \
> -DPKG_PYTHON=ON \
> -DPKG_QEQ=ON \
> -DPKG_REPLICA=ON \
> -DPKG_RIGID=ON \
> -DPKG_SHOCK=ON \
> -DPKG_SNAP=ON \
> -DPKG_SRD=ON \
> -DPKG_USER-ATC=ON \
> -DPKG_USER-AWPMD=ON \
> -DPKG_USER-BOCS=ON \
> -DPKG_USER-CGDNA=ON \
> -DPKG_USER-CGSDK=ON \
> -DPKG_USER-DIFFRACTION=ON \
> -DPKG_USER-DPD=ON \
> -DPKG_USER-DRUDE=ON \
> -DPKG_USER-EFF=ON \
> -DPKG_USER-FEP=ON \
> -DPKG_USER-H5MD=ON \
> -DPKG_USER-LB=ON \
> -DPKG_USER-MANIFOLD=ON \
> -DPKG_USER-MEAMC=ON \
> -DPKG_USER-MGPT=ON \
> -DPKG_USER-MISC=ON \
> -DPKG_USER-MOFFF=ON \
> -DPKG_USER-MOLFILE=ON \
> -DPKG_USER-NETCDF=ON \
> -DPKG_USER-OMP=ON \
> -DPKG_USER-PHONON=ON \
> -DPKG_USER-QTB=ON \
> -DPKG_USER-REAXC=OFF \
> -DPKG_USER-SMD=ON \
> -DPKG_USER-SMTBQ=ON \
> -DPKG_USER-SPH=ON \
> -DPKG_USER-TALLY=ON \
> -DPKG_USER-UEF=ON \
> -DPKG_USER-VTK=ON \
> -DPKG_VORONOI=ON
> cd debian/build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_SHARED_LIBS=ON -DCMAKE_SKIP_INSTALL_RPATH=TRUE -DPKG_ASPHERE=ON -DPKG_BODY=ON -DPKG_CLASS2=ON -DPKG_COLLOID=ON -DPKG_COMPRESS=ON -DPKG_CORESHELL=ON -DPKG_EXTRA-PAIR=ON -DPKG_DIPOLE=ON -DPKG_GPU=OFF -DPKG_GRANULAR=ON -DPKG_KIM=ON -DPKG_KSPACE=ON -DPKG_MANYBODY=ON -DPKG_MC=ON -DPKG_MISC=ON -DPKG_MOLECULE=ON -DPKG_MPIIO=ON -DPKG_OPT=ON
> -DPKG_PERI=ON -DPKG_POEMS=ON -DPKG_PYTHON=ON -DPKG_QEQ=ON -DPKG_REPLICA=ON -DPKG_RIGID=ON -DPKG_SHOCK=ON -DPKG_SNAP=ON -DPKG_SRD=ON -DPKG_USER-ATC=ON -DPKG_USER-AWPMD=ON -DPKG_USER-BOCS=ON -DPKG_USER-CGDNA=ON -DPKG_USER-CGSDK=ON -DPKG_USER-DIFFRACTION=ON -DPKG_USER-DPD=ON -DPKG_USER-DRUDE=ON -DPKG_USER-EFF=ON -DPKG_USER-FEP=ON -DPKG_USER-H5MD=ON -DPKG_USER-LB=ON -DPKG_USER-MANIFOLD=ON -DPKG_USER-MEAMC=ON -DPKG_USER-MGPT=ON -DPKG_USER-MISC=ON -DPKG_USER-MOFFF=ON -DPKG_USER-MOLFILE=ON -DPKG_USER-NETCDF=ON -DPKG_USER-OMP=ON -DPKG_USER-PHONON=ON -DPKG_USER-QTB=ON -DPKG_USER-REAXC=OFF -DPKG_USER-SMD=ON -DPKG_USER-SMTBQ=ON -DPKG_USER-SPH=ON -DPKG_USER-TALLY=ON -DPKG_USER-UEF=ON -DPKG_USER-VTK=ON -DPKG_VORONOI=ON ../../cmake
> CMake Deprecation Warning at CMakeLists.txt:13 (cmake_policy):
> The OLD behavior for policy CMP0109 will be removed from a future version
> of CMake.
>
> The cmake-policies(7) manual explains that the OLD behaviors of all
> policies are deprecated and that a policy should be set to OLD only under
> specific short-term circumstances. Projects should be ported to the NEW
> behavior and not rely on setting a policy to OLD.
>
>
> -- The CXX compiler identification is GNU 13.2.0
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/c++ - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Found Git: /usr/bin/git (found version "2.40.1")
> -- Running check for auto-generated files from make-based build system
> -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
> -- Found MPI: TRUE (found version "3.1")
> -- Looking for C++ include omp.h
> -- Looking for C++ include omp.h - found
> -- Found OpenMP_CXX: -fopenmp (found version "4.5")
> -- Found OpenMP: TRUE (found version "4.5")
> -- Found JPEG: /usr/lib/x86_64-linux-gnu/libjpeg.so (found version "62")
> -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.40")
> -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13")
> -- Found GZIP: /bin/gzip
> -- Could NOT find FFMPEG (missing: FFMPEG_EXECUTABLE)
> -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
> -- Checking for module 'fftw3'
> -- Found fftw3, version 3.3.10
> -- Found FFTW3: /usr/lib/x86_64-linux-gnu/libfftw3.so
> -- Found Python: /usr/include/python3.11 (found version "3.11.4") found components: Development Development.Module Development.Embed
> -- Found VORO: /usr/lib/x86_64-linux-gnu/libvoro++.so
> -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.2.1")
> -- Found KIM-API: /usr/lib/x86_64-linux-gnu/libkim-api.so.2.3.0
> -- Checking for module 'libzstd>=1.4'
> -- Found libzstd, version 1.5.5
> -- Looking for C++ include cmath
> -- Looking for C++ include cmath - found
> -- Generating style headers...
> -- Generating package headers...
> -- Generating lmpinstalledpkgs.h...
> -- Found Python: /usr/bin/python3 (found version "3.11.4") found components: Interpreter
> -- Could NOT find ClangFormat (missing: ClangFormat_EXECUTABLE) (Required is at least version "8.0")
> -- The following tools and libraries have been found and configured:
> * Git
> * MPI
> * OpenMP
> * JPEG
> * PNG
> * FFTW3
> * VORO
> * CURL
> * KIM-API (required version >= 2.2.0)
> * ZLIB
> * PkgConfig
> * Python
>
> -- <<< Build configuration >>>
> Operating System: Linux Debian GNU/Linux
> Build type: None
> Install path: /usr
> Generator: Unix Makefiles using /usr/bin/gmake
> -- Enabled packages: ASPHERE;BODY;CLASS2;COLLOID;COMPRESS;CORESHELL;DIPOLE;EXTRA-PAIR;GRANULAR;KIM;KSPACE;MANYBODY;MC;MISC;MOLECULE;MPIIO;OPT;PERI;POEMS;PYTHON;QEQ;REPLICA;RIGID;SHOCK;SRD;VORONOI
> -- <<< Compilers and Flags: >>>
> -- C++ Compiler: /usr/bin/c++
> Type: GNU
> Version: 13.2.0
> C++ Flags: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
> Defines: LAMMPS_SMALLBIG;LAMMPS_MEMALIGN=64;LAMMPS_OMP_COMPAT=4;LAMMPS_JPEG;LAMMPS_PNG;LAMMPS_GZIP;FFT_FFTW3;FFT_FFTW_THREADS;LMP_PYTHON;LMP_KIM_CURL;LAMMPS_ZSTD;LMP_MPIIO
> -- <<< Linker flags: >>>
> -- Executable name: lmp
> -- Executable linker flags: -Wl,-z,relro
> -- Shared library flags: -Wl,-z,relro
> -- <<< MPI flags >>>
> -- MPI_defines: MPICH_SKIP_MPICXX;OMPI_SKIP_MPICXX;_MPICC_H
> -- MPI includes: /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
> -- MPI libraries: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;
> -- <<< FFT settings >>>
> -- Primary FFT lib: FFTW3
> -- Using double precision FFTs
> -- Using threaded FFTs
> -- Configuring done (8.3s)
> -- Generating done (0.2s)
> CMake Warning:
> Manually-specified variables were not used by the project:
>
> CMAKE_EXPORT_NO_PACKAGE_REGISTRY
> CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
> FETCHCONTENT_FULLY_DISCONNECTED
> PKG_SNAP
> PKG_USER-ATC
> PKG_USER-AWPMD
> PKG_USER-BOCS
> PKG_USER-CGDNA
> PKG_USER-CGSDK
> PKG_USER-DIFFRACTION
> PKG_USER-DPD
> PKG_USER-DRUDE
> PKG_USER-EFF
> PKG_USER-FEP
> PKG_USER-H5MD
> PKG_USER-LB
> PKG_USER-MANIFOLD
> PKG_USER-MEAMC
> PKG_USER-MGPT
> PKG_USER-MISC
> PKG_USER-MOFFF
> PKG_USER-MOLFILE
> PKG_USER-NETCDF
> PKG_USER-OMP
> PKG_USER-PHONON
> PKG_USER-QTB
> PKG_USER-REAXC
> PKG_USER-SMD
> PKG_USER-SMTBQ
> PKG_USER-SPH
> PKG_USER-TALLY
> PKG_USER-UEF
> PKG_USER-VTK
>
>
> -- Build files have been written to: /<<PKGBUILDDIR>>/debian/build
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> debian/rules override_dh_auto_build-indep
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> cd /<<PKGBUILDDIR>>/doc && mkdir html && /usr/bin/make html
> mkdir: cannot create directory ‘html’: File exists
> make[1]: *** [debian/rules:75: override_dh_auto_build-indep] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:10: build] Error 2
> dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/lammps_20220106.git7586adbb6a+ds1-2_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.
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