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Build fails on WSL Ubuntu 24 #1994

Open
juanlm-verus opened this issue Jan 23, 2025 · 7 comments
Open

Build fails on WSL Ubuntu 24 #1994

juanlm-verus opened this issue Jan 23, 2025 · 7 comments

Comments

@juanlm-verus
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Following up from #1981

Running WSL2


Distributor ID: Ubuntu
Description:    Ubuntu 24.04.1 LTS
Release:        24.04
Codename:       noble

Following instructions as described in the INSTALL.md file:


$ mkdir build
$ cd build
$ cmake ..
$ make check # (optional, runs unit tests)
$ make install

I get the following:


juan@XLS-LT-482PCC:/mnt/c/Users/juan.lopera/gtsam$ mkdir build && cd build
juan@XLS-LT-482PCC:/mnt/c/Users/juan.lopera/gtsam/build$ cmake ..
-- The CXX compiler identification is GNU 13.3.0
-- The C compiler identification is GNU 13.3.0
-- 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
-- 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
-- GTSAM_POSE3_EXPMAP=ON, enabling GTSAM_ROT3_EXPMAP as well
-- Performing Test COMPILER_HAS_WSUGGEST_OVERRIDE
-- Performing Test COMPILER_HAS_WSUGGEST_OVERRIDE - Success
-- Performing Test COMPILER_HAS_WMISSING_OVERRIDE
-- Performing Test COMPILER_HAS_WMISSING_OVERRIDE - Failed
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.65") found components: serialization system filesystem thread program_options date_time timer chrono regex 
-- Found Eigen version: 3.4.0
CMake Deprecation Warning at gtsam/3rdparty/metis/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for getline
-- Looking for getline - found
-- checking for thread-local storage - found
-- Could NOT find MKL (missing: MKL_INCLUDE_DIR MKL_LIBRARIES) 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Building 3rdparty
-- Could NOT find GeographicLib (missing: GeographicLib_LIBRARY_DIRS GeographicLib_LIBRARIES GeographicLib_INCLUDE_DIRS) 
-- Building base
-- Building basis
-- Building constrained
-- Building geometry
-- Building inference
-- Building symbolic
-- Building discrete
-- Building hybrid
-- Building linear
-- Building nonlinear
-- Building sam
-- Building sfm
-- Building slam
-- Building navigation
-- GTSAM Version: 4.3a0
-- Install prefix: /usr/local
-- Building GTSAM - as a SHARED library
-- Building base_unstable
-- Building geometry_unstable
-- Building linear_unstable
-- Building discrete_unstable
-- Building dynamics_unstable
-- Building nonlinear_unstable
-- Building slam_unstable
-- Building partition_unstable
-- GTSAM_UNSTABLE Version: 4.3a0
-- Install prefix: /usr/local
-- Wrote /mnt/c/Users/juan.lopera/gtsam/build/GTSAMConfig.cmake
-- Wrote /mnt/c/Users/juan.lopera/gtsam/build/GTSAM_UNSTABLEConfig.cmake
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- ===============================================================
-- ================  Configuration Options  ======================
--  CMAKE_CXX_COMPILER_ID type                       : GNU
--  CMAKE_CXX_COMPILER_VERSION                       : 13.3.0
--  CMake version                                    : 3.28.3
--  CMake generator                                  : Unix Makefiles
--  CMake build tool                                 : /usr/bin/gmake
-- Build flags                                               
--  Build Tests                                      : Enabled
--  Build examples with 'make all'                   : Enabled
--  Build timing scripts with 'make all'             : Disabled
--  Build shared GTSAM libraries                     : Enabled
--  Put build type in library name                   : Enabled
--  Build libgtsam_unstable                          : Enabled
--  Build GTSAM unstable Python                      : Enabled
--  Build MATLAB Toolbox for unstable                : Disabled
--  Build for native architecture                    : Disabled
--  Build type                                       : Release
--  C compilation flags                              :  -O3 -DNDEBUG
--  C++ compilation flags                            :  -O3 -DNDEBUG
--  Enable Boost serialization                       : ON
--  GTSAM_COMPILE_FEATURES_PUBLIC                    : cxx_std_17
--  GTSAM_COMPILE_OPTIONS_PUBLIC                     : 
--  GTSAM_COMPILE_DEFINITIONS_PUBLIC                 : 
--  GTSAM_COMPILE_OPTIONS_PUBLIC_RELEASE             : 
--  GTSAM_COMPILE_DEFINITIONS_PUBLIC_RELEASE         : 
--  Use System Eigen                                 : OFF (Using version: 3.4.0)
--  Use System Metis                                 : OFF
--  Using Boost version                              : 1.83.0
--  Use Intel TBB                                    : Yes (Version: 2021.11.0)
--  Eigen will use MKL                               : MKL not found
--  Eigen will use MKL and OpenMP                    : OpenMP found but GTSAM_WITH_EIGEN_MKL is disabled
--  Default allocator                                : TBB
--  Cheirality exceptions enabled                    : YES
--  Build with ccache                                : Yes
-- Packaging flags
--  CPack Source Generator                           : TGZ
--  CPack Generator                                  : TGZ
-- GTSAM flags                                               
--  Quaternions as default Rot3                      : Disabled
--  Runtime consistency checking                     : Disabled
--  Build with Memory Sanitizer                      : Disabled
--  Rot3 retract is full ExpMap                      : Enabled
--  Pose3 retract is full ExpMap                     : Enabled
--  Enable branch merging in DecisionTree            : Enabled
--  Enable timing machinery                          : Disabled
--  Allow features deprecated in GTSAM 4.3           : Enabled
--  Metis-based Nested Dissection                    : Enabled
--  Use tangent-space preintegration                 : Enabled
-- MATLAB toolbox flags
--  Install MATLAB toolbox                           : Disabled
-- Python toolbox flags                                      
--  Build Python module with pybind                  : Disabled
-- ===============================================================
-- Configuring done (11.2s)
-- Generating done (65.8s)
-- Build files have been written to: /mnt/c/Users/juan.lopera/gtsam/build
juan@XLS-LT-482PCC:/mnt/c/Users/juan.lopera/gtsam/build$ make install
[  2%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/b64.c.o
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[  2%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/csr.c.o
[  2%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/error.c.o
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[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/memory.c.o
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[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/pdb.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/pqueue.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/random.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/rw.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/seq.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/sort.c.o
[  4%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/__/GKlib/string.c.o
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[  9%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/initpart.c.o
[  9%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/kmetis.c.o
[  9%] Building C object gtsam/3rdparty/metis/libmetis/CMakeFiles/metis-gtsam.dir/kwayfm.c.o
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[ 68%] Building CXX object gtsam/CMakeFiles/gtsam.dir/navigation/GPSFactor.cpp.o
[ 68%] Building CXX object gtsam/CMakeFiles/gtsam.dir/navigation/ImuBias.cpp.o
[ 68%] Building CXX object gtsam/CMakeFiles/gtsam.dir/navigation/ImuFactor.cpp.o
[ 68%] Building CXX object gtsam/CMakeFiles/gtsam.dir/navigation/ManifoldPreintegration.cpp.o
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[ 68%] Building CXX object gtsam/CMakeFiles/gtsam.dir/navigation/TangentPreintegration.cpp.o
[ 68%] Linking CXX shared library libgtsam.so
[ 68%] Built target gtsam
[ 68%] Building CXX object examples/CMakeFiles/CameraResectioning.dir/CameraResectioning.cpp.o
[ 68%] Linking CXX executable CameraResectioning
[ 68%] Built target CameraResectioning
[ 68%] Building CXX object examples/CMakeFiles/CombinedImuFactorsExample.dir/CombinedImuFactorsExample.cpp.o
In file included from /mnt/c/Users/juan.lopera/gtsam/gtsam/base/Testable.h:36,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam/inference/Symbol.h:21,
                 from /mnt/c/Users/juan.lopera/gtsam/examples/CombinedImuFactorsExample.cpp:39:
/mnt/c/Users/juan.lopera/gtsam/gtsam/base/concepts.h:20: error: "BOOST_CONCEPT_USAGE" redefined [-Werror]
   20 | #define BOOST_CONCEPT_USAGE(concept) void check##concept()
      | 
In file included from /usr/include/boost/concept_check.hpp:31,
                 from /usr/include/boost/range/concepts.hpp:19,
                 from /usr/include/boost/range/size_type.hpp:20,
                 from /usr/include/boost/range/size.hpp:21,
                 from /usr/include/boost/range/functions.hpp:20,
                 from /usr/include/boost/range/iterator_range_core.hpp:38,
                 from /usr/include/boost/lexical_cast.hpp:48,
                 from /usr/include/boost/program_options/value_semantic.hpp:14,
                 from /usr/include/boost/program_options/options_description.hpp:13,
                 from /usr/include/boost/program_options.hpp:15,
                 from /mnt/c/Users/juan.lopera/gtsam/examples/CombinedImuFactorsExample.cpp:36:
/usr/include/boost/concept/usage.hpp:35: note: this is the location of the previous definition
   35 | #   define BOOST_CONCEPT_USAGE(model)                                    \
      | 
cc1plus: all warnings being treated as errors
make[2]: *** [examples/CMakeFiles/CombinedImuFactorsExample.dir/build.make:76: examples/CMakeFiles/CombinedImuFactorsExample.dir/CombinedImuFactorsExample.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:23462: examples/CMakeFiles/CombinedImuFactorsExample.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

The previous issue #1981 was closed so I'm assuming that the build did succeed after merging the changes.
@ArkadiuszNiemiec ArkadiuszNiemiec mentioned this issue Jan 23, 2025
Merged
@ArkadiuszNiemiec
Copy link

Faced the same issue. From what I understand the GTSAM_USE_BOOST_FEATURES identifier/macro check in:

gtsam/gtsam/base/concepts.h

Lines 11 to 24 in 7b56d66

#if GTSAM_USE_BOOST_FEATURES
#include <boost/concept_check.hpp>
#include <boost/concept/assert.hpp>
#include <boost/concept/requires.hpp>
#include <boost/concept_check.hpp>
#define GTSAM_CONCEPT_ASSERT(concept) BOOST_CONCEPT_ASSERT((concept))
#define GTSAM_CONCEPT_REQUIRES(concept, return_type) BOOST_CONCEPT_REQUIRES(((concept)), (return_type))
#else
// This does something sensible:
#define BOOST_CONCEPT_USAGE(concept) void check##concept()
// These just ignore the concept checking for now:
#define GTSAM_CONCEPT_ASSERT(concept) static_assert(true, "")
#define GTSAM_CONCEPT_REQUIRES(concept, return_type) return_type
#endif

...will always fail as it's never set in CMakeLists.txt.

The #1995 includes a potential fix, please test it.

@juanlm-verus
Copy link
Author

Hi Arkadiusz,

Thanks for the potential fix. It does seem to fix the initial error I reported as the build then proceeds passed the point at which it failed for me. However, I then seem to run into a new issue:


[ 92%] Linking CXX executable VisualISAM2Example
[ 92%] Built target VisualISAM2Example
[ 92%] Linking CXX executable SolverComparer
[ 92%] Built target SolverComparer
In file included from /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/util/ConfigureVectorization.h:346,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/Core:22,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/Dense:1,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam/base/OptionalJacobian.h:24,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam/base/Matrix.h:27,
                 from /mnt/c/Users/juan.lopera/gtsam/gtsam_unstable/linear/QPSParser.cpp:20:
In function ‘void _mm_store_pd(double*, __m128d)’,
    inlined from ‘void Eigen::internal::pstore(Scalar*, const Packet&) [with Scalar = double; Packet = __vector(2) double]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/arch/SSE/PacketMath.h:790:126,
    inlined from ‘void Eigen::internal::pstoret(Scalar*, const Packet&) [with Scalar = double; Packet = __vector(2) double; int Alignment = 16]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/GenericPacketMath.h:978:11,
    inlined from ‘void Eigen::internal::assign_op<DstScalar, SrcScalar>::assignPacket(DstScalar*, const Packet&) const [with int Alignment = 16; Packet = __vector(2) double; DstScalar = double; SrcScalar = double]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/functors/AssignmentFunctors.h:28:50,
    inlined from ‘void Eigen::internal::generic_dense_assignment_kernel<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignPacket(Eigen::Index, Eigen::Index) [with int StoreMode = 16; int LoadMode = 0; PacketType = __vector(2) double; DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, -1, -1> >; Functor = Eigen::internal::assign_op<double, double>; int Version = 0]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:675:47,
    inlined from ‘void Eigen::internal::generic_dense_assignment_kernel<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignPacketByOuterInner(Eigen::Index, Eigen::Index) [with int StoreMode = 16; int LoadMode = 0; PacketType = __vector(2) double; DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Matrix<double, -1, -1> >; Functor = Eigen::internal::assign_op<double, double>; int Version = 0]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:689:48,
    inlined from ‘static void Eigen::internal::dense_assignment_loop<Kernel, 4, 0>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false> >, Eigen::internal::evaluator<Eigen::Matrix<double, -1, -1> >, Eigen::internal::assign_op<double, double>, 0>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:572:86,
    inlined from ‘void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; SrcXprType = Eigen::Matrix<double, -1, -1>; Functor = assign_op<double, double>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:785:37,
    inlined from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; SrcXprType = Eigen::Matrix<double, -1, -1>; Functor = Eigen::internal::assign_op<double, double>; Weak = void]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:954:31,
    inlined from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; Src = Eigen::Matrix<double, -1, -1>; Func = assign_op<double, double>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:890:49,
    inlined from ‘void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing<Src>::value), void*>::type) [with Dst = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; Src = Eigen::Matrix<double, -1, -1>; Func = assign_op<double, double>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:858:27,
    inlined from ‘void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; Src = Eigen::Matrix<double, -1, -1>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:836:18,
    inlined from ‘Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Matrix<double, -1, -1>; Derived = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/Assign.h:66:28,
    inlined from ‘void gtsam::JacobianFactor::fillTerms(const TERMS&, const gtsam::Vector&, const gtsam::SharedDiagonal&) [with TERMS = std::map<long unsigned int, Eigen::Matrix<double, 1, 1, 0, 1, 1> >]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/linear/JacobianFactor-inl.h:94:14:
/usr/lib/gcc/x86_64-linux-gnu/13/include/emmintrin.h:169:19: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ reading 16 or more bytes from a region of size 8 [-Werror=stringop-overread]
  169 |   *(__m128d *)__P = __A;
      |   ~~~~~~~~~~~~~~~~^~~~~
In file included from /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/Core:166:
In function ‘void* Eigen::internal::aligned_malloc(std::size_t)’,
    inlined from ‘void* Eigen::internal::conditional_aligned_malloc(std::size_t) [with bool Align = true]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/util/Memory.h:241:24,
    inlined from ‘T* Eigen::internal::conditional_aligned_new_auto(std::size_t) [with T = double; bool Align = true]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/util/Memory.h:404:69,
    inlined from ‘void Eigen::DenseStorage<T, -1, -1, -1, _Options>::resize(Eigen::Index, Eigen::Index, Eigen::Index) [with T = double; int _Options = 0]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/DenseStorage.h:486:85,
    inlined from ‘void Eigen::PlainObjectBase<Derived>::resize(Eigen::Index, Eigen::Index) [with Derived = Eigen::Matrix<double, -1, -1>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/PlainObjectBase.h:285:25,
    inlined from ‘void Eigen::internal::resize_if_allowed(DstXprType&, const SrcXprType&, const assign_op<T1, T2>&) [with DstXprType = Eigen::Matrix<double, -1, -1>; SrcXprType = Eigen::Matrix<double, 1, 1, 0, 1, 1>; T1 = double; T2 = double]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:764:15,
    inlined from ‘void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, -1, -1>; SrcXprType = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Functor = assign_op<double, double>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:778:20,
    inlined from ‘static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Matrix<double, -1, -1>; SrcXprType = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Functor = Eigen::internal::assign_op<double, double>; Weak = void]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:954:31,
    inlined from ‘void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Matrix<double, -1, -1>; Src = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Func = assign_op<double, double>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/AssignEvaluator.h:890:49,
    inlined from ‘Derived& Eigen::PlainObjectBase<Derived>::_set_noalias(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Derived = Eigen::Matrix<double, -1, -1>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/PlainObjectBase.h:797:41,
    inlined from ‘void Eigen::PlainObjectBase<Derived>::_init1(const Eigen::DenseBase<ElseDerived>&) [with T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; OtherDerived = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Derived = Eigen::Matrix<double, -1, -1>]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/PlainObjectBase.h:883:25,
    inlined from ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T&) [with T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; _Scalar = double; int _Rows = -1; int _Cols = -1; int _Options = 0; int _MaxRows = -1; int _MaxCols = -1]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/Matrix.h:332:31,
    inlined from ‘constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = Eigen::Matrix<double, 1, 1, 0, 1, 1>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = Eigen::Matrix<double, -1, -1>]’ at /usr/include/c++/13/bits/stl_pair.h:586:22,
    inlined from ‘void gtsam::JacobianFactor::fillTerms(const TERMS&, const gtsam::Vector&, const gtsam::SharedDiagonal&) [with TERMS = std::map<long unsigned int, Eigen::Matrix<double, 1, 1, 0, 1, 1> >]’ at /mnt/c/Users/juan.lopera/gtsam/gtsam/linear/JacobianFactor-inl.h:84:37:
/mnt/c/Users/juan.lopera/gtsam/gtsam/3rdparty/Eigen/Eigen/src/Core/util/Memory.h:182:20: note: source object of size 8 allocated by ‘malloc’
  182 |     result = malloc(size);
      |              ~~~~~~^~~~~~
cc1plus: all warnings being treated as errors
make[2]: *** [gtsam_unstable/CMakeFiles/gtsam_unstable.dir/build.make:188: gtsam_unstable/CMakeFiles/gtsam_unstable.dir/linear/QPSParser.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:28025: gtsam_unstable/CMakeFiles/gtsam_unstable.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

Perhaps the -Werror=stringop-overread should also be ignored in other locations as it is in testFourier.cpp after the fixes in #1978

Are you also running into this issue?

@ArkadiuszNiemiec
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ArkadiuszNiemiec commented Jan 24, 2025 •
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No, I didn't have this error, sorry...
BTW. The fix was working, but there was a better way to do it. I've updated the PR.

Looks like you are using gcc 13.3.0, that's fairly new version. Mine is still 9.4.0. I would try updating with apt upgrade, or downgrading the gcc...

@juanlm-verus
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Thanks Arkadiusz I'll try that out!

@ArkadiuszNiemiec
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Did a quick installation of WSL Ubuntu-24.04 and can confirm: the issue is there with the gcc 13.3.0. Updating the gcc to 14.2 didn't help. Guess the issue is with the newer compilers and the Eigen lib. Maybe new versions of Eigen already fixed that?

@juanlm-verus You can try to downgrade the gcc or install older Ubuntu. I'm using Ubuntu-20.04, 22.04 might work as well.

@juanlm-verus
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I'm currently trying with GCC 9.5 on Ubuntu 24.04. I'll also get back here on how that goes. If that fails I will try with an older version of Ubuntu. Thanks Arkadiusz

@ProfFan
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ProfFan commented Jan 25, 2025

You can use a later version of Eigen, just install it and have GTSAM use system Eigen.

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