Bug#1084255: fenics-dolfinx: FTBFS: The imported target "adios2::EncryptionOperator" references the file "/usr/lib/x86_64-linux-gnu/adios2/mpi/plugins/libEncryptionOperator.so" but this file does not exist.
Santiago Vila
sanvila at debian.org
Mon Oct 7 09:30:25 BST 2024
Package: src:fenics-dolfinx
Version: 1:0.8.0-11
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem=cmake --with python3,sphinxdoc
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
PETSC_DIR=/usr/lib/petscdir/petsc3.20/x86_64-linux-gnu-real SLEPC_DIR=/usr/lib/slepcdir/slepc3.20/x86_64-linux-gnu-real dh_auto_configure --builddir=/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu-real -D/<<PKGBUILDDIR>>/cpp -- -D CMAKE_BUILD_TYPE:STRING=RelWithDebInfo -D BUILD_SHARED_LIBS:BOOL=ON -D CMAKE_SKIP_RPATH:BOOL=ON -D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF -D DOLFINX_ENABLE_TRILINOS:BOOL=OFF -D DOLFINX_ENABLE_HDF5:BOOL=ON -D HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5pcc -D DOLFINX_ENABLE_PARMETIS:BOOL=OFF -D DOLFINX_ENABLE_SCOTCH:BOOL=ON -D DOLFINX_ENABLE_DOCS:BOOL=OFF -D DOLFINX_ENABLE_MPI:BOOL=ON -D MPIEXEC_PARAMS:STRING="--oversubscribe" -D CMAKE_CXX_FLAGS:STRING="-fpermissive" -D DOLFINX_EXTRA_CXX_FLAGS:STRING="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" -D DEBIAN_VERSION_ID=debian_1:0.8.0-11
cd obj-x86_64-linux-gnu-real && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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 -D CMAKE_BUILD_TYPE:STRING=RelWithDebInfo -D BUILD_SHARED_LIBS:BOOL=ON -D CMAKE_SKIP_RPATH:BOOL=ON -D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF -D DOLFINX_ENABLE_TRILINOS:BOOL=OFF -D DOLFINX_ENABLE_HDF5:BOOL=ON -D HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5pcc -D DOLFINX_ENABLE_PARMETIS:BOOL=OFF -D DOLFINX_ENABLE_SCOTCH:BOOL=ON -D DOLFINX_ENABLE_DOCS:BOOL=OFF -D DOLFINX_ENABLE_MPI:BOOL=ON -D MPIEXEC_PARAMS:STRING=--oversubscribe -D CMAKE_CXX_FLAGS:STRING=-fpermissive -D "DOLFINX_EXTRA_CXX_FLAGS:STRING=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" -D DEBIAN_VERSION_ID=debian_1:0.8.0-11 ../cpp
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- 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 MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found suitable version "3.1", minimum required is "3")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found suitable version "3.1", minimum required is "3")
-- Found MPI: TRUE (found suitable version "3.1", minimum required is "3")
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
CMake Warning (dev) at CMakeLists.txt:274 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost 1.83.0 at /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0
-- Requested configuration: QUIET REQUIRED COMPONENTS timer
-- Found boost_headers 1.83.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_headers-1.83.0
-- Found boost_timer 1.83.0 at /usr/lib/x86_64-linux-gnu/cmake/boost_timer-1.83.0
-- [x] libboost_timer.so.1.83.0
-- [ ] libboost_timer.a
-- Adding boost_timer dependencies: headers
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.70") found components: timer
-- Checking for basix hints with /usr/bin/python3
-- Adding /usr/lib/python3/dist-packages/basix to Basix search hints
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.10") found components: C
-- HDF5_DIR: HDF5_DIR-NOTFOUND
-- HDF5_DEFINITIONS:
-- HDF5_INCLUDE_DIRS: /usr/include/hdf5/openmpi
-- HDF5_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_HL_LIBRARIES:
-- HDF5_C_DEFINITIONS:
-- HDF5_C_INCLUDE_DIR:
-- HDF5_C_INCLUDE_DIRS: /usr/include/hdf5/openmpi
-- HDF5_C_LIBRARY:
-- HDF5_C_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_C_HL_LIBRARY:
-- HDF5_C_HL_LIBRARIES:
-- Defined targets (if any):
-- ... hdf5::hdf5
-- Found Python3: /usr/bin/python3 (found version "3.12.7") found components: Interpreter
-- Asking Python module FFCx for location of UFC... (Python executable: /usr/bin/python3)
-- Found UFCx: /usr/lib/python3/dist-packages/ffcx/codegeneration (found suitable version "0.8.0", minimum required is "0.8")
-- Found ADIOS2: /usr/lib/x86_64-linux-gnu/cmake/adios2/mpi/adios2-config.cmake (found suitable version "2.10.1", minimum required is "2.8.1") found components: CXX
CMake Error at /usr/lib/x86_64-linux-gnu/cmake/adios2/mpi/adios2-targets.cmake:137 (message):
The imported target "adios2::EncryptionOperator" references the file
"/usr/lib/x86_64-linux-gnu/adios2/mpi/plugins/libEncryptionOperator.so"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
"/usr/lib/x86_64-linux-gnu/cmake/adios2/mpi/adios2-targets.cmake"
but not all the files it references.
Call Stack (most recent call first):
/usr/lib/x86_64-linux-gnu/cmake/adios2/mpi/adios2-config-common.cmake:214 (include)
/usr/lib/x86_64-linux-gnu/cmake/adios2/mpi/adios2-config.cmake:29 (include)
/usr/lib/x86_64-linux-gnu/cmake/adios2/adios2-config.cmake:9 (include)
CMakeLists.txt:366 (find_package)
-- Configuring incomplete, errors occurred!
cd obj-x86_64-linux-gnu-real && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu-real
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# If you do not want to change any of the values, simply exit the editor.
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//No help, variable specified on the command line.
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dh_auto_configure: error: cd obj-x86_64-linux-gnu-real && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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 -D CMAKE_BUILD_TYPE:STRING=RelWithDebInfo -D BUILD_SHARED_LIBS:BOOL=ON -D CMAKE_SKIP_RPATH:BOOL=ON -D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF -D DOLFINX_ENABLE_TRILINOS:BOOL=OFF -D DOLFINX_ENABLE_HDF5:BOOL=ON -D HDF5_C_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5pcc -D DOLFINX_ENABLE_PARMETIS:BOOL=OFF -D DOLFINX_ENABLE_SCOTCH:BOOL=ON -D DOLFINX_ENABLE_DOCS:BOOL=OFF -D DOLFINX_ENABLE_MPI:BOOL=ON -D MPIEXEC_PARAMS:STRING=--oversubscribe -D CMAKE_CXX_FLAGS:STRING=-fpermissive -D "DOLFINX_EXTRA_CXX_FLAGS:STRING=-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" -D DEBIAN_VERSION_ID=debian_1:0.8.0-11 ../cpp returned exit code 1
make[1]: *** [debian/rules:177: override_dh_auto_configure] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:161: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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