error related to numpy version

[AiweiWu]

cellphonedb can be installed successfully by running command "pip install -U cellphonedb", but the following step failed when running "cellphonedb database download", raising an error: ValueError: "numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject", others suggested to update the numpy from v1.19.5 to the latest version, it works.

I noticed that cellphonedb 3.1.0 requires numpy<=1.19.5,>=1.16.5, maybe the requirement "numpy<=1.19.5" can be removed.

[prete]

Hi @AiweiWu, thank you for your input. We're in the process of updating CellPhoneDB for a new release and will consider removing those limits or at least using a latter version of packages.

Which python version are you using? (python -V) more recent python versions may yield other errors (3.10/3.11)

For the time beeing, you can try this workaround: (a) uninstall your current cellphonedb (b) copy the requirements.txt to your environment (c) edit the file to increase numpy's upper limit for the package (ie numpy<=1.20.3,>=1.16.5) (d) install the dependenices using pip install -r requirements.txt (e) install cellphonedb without checking dependenices pip install -U cellphonedb --no-dependencies

Let us know if that works for you.

[AiweiWu]

Hi, Thanks for your reply.

The python version I'm using is 3.11.0, and the version of conda and pip are 22.9.0 and 22.3.1, repectively.

I followed your all suggestions, and in step (c), I increse numpy's upper limit for the package (numpy<=1.20.3,>=1.16.5) but it does not work (error in step d), installing Cython (>=0.28.5) and scikit-learn helps me go through workaround.

At 2022-11-21 18:18:45, "Prete" @.***> wrote:

Hi @AiweiWu, thank you for your input. We're in the process of updating CellPhoneDB for a new release and will consider removing those limits or at least using a latter version of packages.

Which python version are you using? (python -V) more recent python versions may yield other errors (3.10/3.11)

For the time beeing, you can try this workaround: (a) uninstall your current cellphonedb (b) copy the requirements.txt to your environment (c) edit the file to increase numpy's upper limit for the package (ie numpy<=1.20.3,>=1.16.5) (d) install the dependenices using pip install -r requirements.txt (e) install cellphonedb without checking dependenices pip install -U cellphonedb --no-dependencies

Let us know if that works for you.

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[prete]

Hi @AiweiWu, glad to read ita working now - out of curiosity which version of scikit-learn did you end up with?

[AiweiWu]

The version of scikit-learn is 0.22 (conda activate cpdb && pip list|grep scikit-learn).

At 2022-11-28 18:10:49, "Prete" @.***> wrote:

Hi @AiweiWu, glad to read ita working now - out of curiosity which version of scikit-learn did you end up with?

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[chrsyl]

I have tried to follow these advices for installing cellphonedb on my Mac M2 arm64 with python 3.9.15. It does not work. It could not build a wheel with numpy, 1.23.5 that anaconda arm64 version installs. I uninstalled numpy 1.23.5 and then reinstalled it and then got the message attached from cellphonedb.I tried to install the correct dependencies but did not get cellphonedb to work. Is there a way forward?

.................... Using cached numpy-1.23.5-cp39-cp39-macosx_11_0_arm64.whl (13.4 MB) Installing collected packages: numpy ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. cellphonedb 3.1.0 requires anndata<=0.75,>=0.7, which is not installed. cellphonedb 3.1.0 requires boto3<2.0,>=1.15, which is not installed. cellphonedb 3.1.0 requires flask<2.0.0,>=1.0, which is not installed. cellphonedb 3.1.0 requires Flask-RESTful>=0.3, which is not installed. cellphonedb 3.1.0 requires Flask-Testing>=0.7, which is not installed. cellphonedb 3.1.0 requires geosketch==0.3, which is not installed. cellphonedb 3.1.0 requires h5py<3.0.0, which is not installed. cellphonedb 3.1.0 requires numpy-groupies, which is not installed. cellphonedb 3.1.0 requires pika<2.0,>=1.0.0, which is not installed. cellphonedb 3.1.0 requires PyYAML<6.0,>=5.4, which is not installed. cellphonedb 3.1.0 requires requests<3.0,>=2.25, which is not installed. cellphonedb 3.1.0 requires rpy2<4.0,>=3.4.0, which is not installed. cellphonedb 3.1.0 requires scikit-learn==0.22, which is not installed. cellphonedb 3.1.0 requires tqdm<5.0,>=4.3, which is not installed. cellphonedb 3.1.0 requires click<8.0,>=7.0, but you have click 8.0.0 which is incompatible. cellphonedb 3.1.0 requires numpy<=1.19.5,>=1.16.5, but you have numpy 1.23.5 which is incompatible. cellphonedb 3.1.0 requires SQLAlchemy<1.4,>=1.3, but you have sqlalchemy 1.4.0 which is incompatible. Successfully installed numpy-1.23.5

[rjpbonnal]

In general would be very useful if you may update all the dependencies. Another example is geosketch which has some issue https://github.com/brianhie/geosketch/issues/11 and h5py where newer packages requires the latter version of it.

[chrsyl]

Still, it did not work after modifying all dependencies.14 mars 2023 kl. 18:43 skrev ktroule @.***>: Closed #76 as completed.

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[ktroule]

Sorry for closing this issue. We have a new version of CellPhoneDB which might solve the issues you have pointed to. Read the documentation, and notebooks and try it. Hopefully, this should solve your problems.

[chrsyl]

Thank you so much. I will try that.

14 mars 2023 kl. 19:13 skrev ktroule @.***>:

Sorry for closing this issue. We have a new version of CellPhoneDB which might solve the issues you have pointed to. Read the documentation, and notebooks and try it. Hopefully, this should solve your problems.

— Reply to this email directly, view it on GitHub https://github.com/ventolab/CellphoneDB/issues/76#issuecomment-1468597977, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXFFRBSDOKJTGOQB45XA6LW4CYNDANCNFSM6AAAAAAR5GQXCY. You are receiving this because you commented.

[chrsyl]

Helo, Unfortunately it is not possible to load cellphonedb on my arm M2 Mac using a Conda environment. No update compared to previous instructions. Best Christer Sylvén ———————— Using conda: conda create -n cpdb python=3.8 Using virtualenv: python -m venv cpdb Activate environment Using conda: source activate cpdb Using virtualenv: source cpdb/bin/activate Install CellPhoneDB pip install cellphonedb ————————— clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/multiarray/lowlevel_strided_loops.c clang: numpy/core/src/multiarray/nditer_constr.c clang: numpy/core/src/multiarray/refcount.c clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: numpy/core/src/multiarray/scalarapi.c clang: numpy/core/src/multiarray/temp_elide.c clang: numpy/core/src/multiarray/vdot.c clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/loops.cclang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/scalarmath.c

        clang: numpy/core/src/umath/ufunc_object.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/npymath/npy_math.c
        clang: numpy/core/src/common/npy_longdouble.cclang: numpy/core/src/npymath/halffloat.c

        clang: numpy/core/src/common/numpyos.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: /private/var/folders/1g/57wsyq2d1l1__jrtrb0kl3lw0000gn/T/pip-install-o96k_fng/numpy_05d9aa3948644d4b8b6de228dee50d93/numpy/_build_utils/src/apple_sgemv_fix.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/umath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/christersylven/miniforge3/envs/cpdb/include/python3.8 -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -c numpy/core/src/multiarray/alloc.c -o build/temp.macosx-11.0-arm64-cpython-38/numpy/core/src/multiarray/alloc.o -MMD -MF build/temp.macosx-11.0-arm64-cpython-38/numpy/core/src/multiarray/alloc.o.d -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for numpy
    Running setup.py clean for numpy
    error: subprocess-exited-with-error

    × python setup.py clean did not run successfully.
    │ exit code: 1
    ╰─> [10 lines of output]
        Running from numpy source directory.

        `setup.py clean` is not supported, use one of the following instead:

          - `git clean -xdf` (cleans all files)
          - `git clean -Xdf` (cleans all versioned files, doesn't touch
                              files that aren't checked into the git repo)

        Add `--force` to your command to use it anyway if you must (unsupported).

        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed cleaning build dir for numpy
  Failed to build numpy
  Installing collected packages: wheel, setuptools, numpy, Cython, scipy
    Running setup.py install for numpy: started
    Running setup.py install for numpy: finished with status 'error'
    error: subprocess-exited-with-error

    × Running setup.py install for numpy did not run successfully.
    │ exit code: 1
    ╰─> [292 lines of output]
        Running from numpy source directory.

        Note: if you need reliable uninstall behavior, then install
        with pip instead of using `setup.py install`:

          - `pip install .`       (from a git repo or downloaded source
                                   release)
          - `pip install numpy`   (last NumPy release on PyPi)

        blas_opt_info:
        blas_mkl_info:
        customize UnixCCompiler
          libraries mkl_rt not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        blis_info:
        customize UnixCCompiler
          libraries blis not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_info:
        customize UnixCCompiler
        customize UnixCCompiler
          libraries openblas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_blas_threads_info:
        Setting PTATLAS=ATLAS
        customize UnixCCompiler
          libraries tatlas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_blas_info:
        customize UnixCCompiler
          libraries satlas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_blas_threads_info:
        Setting PTATLAS=ATLAS
        customize UnixCCompiler
          libraries ptf77blas,ptcblas,atlas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_blas_info:
        customize UnixCCompiler
          libraries f77blas,cblas,atlas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        accelerate_info:
        customize UnixCCompiler
          libraries accelerate not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
        Library accelerate was not found. Ignoring
        customize UnixCCompiler
          libraries veclib not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
        Library veclib was not found. Ignoring
          FOUND:
            extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
            extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
            define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]

          FOUND:
            extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
            extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
            define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]

        /bin/sh: svnversion: command not found
        non-existing path in 'numpy/distutils': 'site.cfg'
        lapack_opt_info:
        lapack_mkl_info:
        customize UnixCCompiler
          libraries mkl_rt not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_lapack_info:
        customize UnixCCompiler
        customize UnixCCompiler
          libraries openblas not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        openblas_clapack_info:
        customize UnixCCompiler
        customize UnixCCompiler
          libraries openblas,lapack not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        flame_info:
        customize UnixCCompiler
          libraries flame not found in ['/Users/christersylven/miniforge3/envs/cpdb/lib', '/usr/lib']
          NOT AVAILABLE

        atlas_3_10_threads_info:
        Setting PTATLAS=ATLAS
        customize UnixCCompiler
          libraries lapack_atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries tatlas,tatlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries lapack_atlas not found in /usr/lib
        customize UnixCCompiler
          libraries tatlas,tatlas not found in /usr/lib
        <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
          NOT AVAILABLE

        atlas_3_10_info:
        customize UnixCCompiler
          libraries lapack_atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries satlas,satlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries lapack_atlas not found in /usr/lib
        customize UnixCCompiler
          libraries satlas,satlas not found in /usr/lib
        <class 'numpy.distutils.system_info.atlas_3_10_info'>
          NOT AVAILABLE

        atlas_threads_info:
        Setting PTATLAS=ATLAS
        customize UnixCCompiler
          libraries lapack_atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries ptf77blas,ptcblas,atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries lapack_atlas not found in /usr/lib
        customize UnixCCompiler
          libraries ptf77blas,ptcblas,atlas not found in /usr/lib
        <class 'numpy.distutils.system_info.atlas_threads_info'>
          NOT AVAILABLE

        atlas_info:
        customize UnixCCompiler
          libraries lapack_atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries f77blas,cblas,atlas not found in /Users/christersylven/miniforge3/envs/cpdb/lib
        customize UnixCCompiler
          libraries lapack_atlas not found in /usr/lib
        customize UnixCCompiler
          libraries f77blas,cblas,atlas not found in /usr/lib
        <class 'numpy.distutils.system_info.atlas_info'>
          NOT AVAILABLE

          FOUND:
            extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
            extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
            define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]

        /Users/christersylven/miniforge3/envs/cpdb/lib/python3.8/site-packages/setuptools/_distutils/dist.py:265: UserWarning: Unknown distribution option: 'define_macros'
          warnings.warn(msg)
        running install
        /Users/christersylven/miniforge3/envs/cpdb/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        running build
        running config_cc
        unifing config_cc, config, build_clib, build_ext, build commands --compiler options
        running config_fc
        unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
        running build_src
        build_src
        building py_modules sources
        building library "npymath" sources
        get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']'
        customize Gnu95FCompiler
        Found executable /opt/homebrew/bin/gfortran
        customize Gnu95FCompiler
        customize Gnu95FCompiler using config
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64

        compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/christersylven/miniforge3/envs/cpdb/include/python3.8 -c'
        clang: _configtest.c
        clang _configtest.o -o _configtest
        success!
        removing: _configtest.c _configtest.o _configtest.o.d _configtest
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64

        compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/christersylven/miniforge3/envs/cpdb/include/python3.8 -c'
        clang: _configtest.c
        _configtest.c:1:5: warning: incompatible redeclaration of library function 'exp' [-Wincompatible-library-redeclaration]
        int exp (void);
            ^
        _configtest.c:1:5: note: 'exp' is a builtin with type 'double (double)'
        1 warning generated.
        clang _configtest.o -o _configtest
        success!
        removing: _configtest.c _configtest.o _configtest.o.d _configtest
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath' to include_dirs.
        None - nothing done with h_files = ['build/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath/npy_math_internal.h']
        building library "npysort" sources
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/common' to include_dirs.
        None - nothing done with h_files = ['build/src.macosx-11.0-arm64-3.8/numpy/core/src/common/npy_sort.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/common/npy_partition.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/common/npy_binsearch.h']
        building extension "numpy.core._dummy" sources
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/config.h' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/_numpyconfig.h' to sources.
        executing numpy/core/code_generators/generate_numpy_api.py
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__multiarray_api.h' to sources.
        numpy.core - nothing done with h_files = ['build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/config.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/_numpyconfig.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__multiarray_api.h']
        building extension "numpy.core._multiarray_tests" sources
        building extension "numpy.core._multiarray_umath" sources
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/config.h' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/_numpyconfig.h' to sources.
        executing numpy/core/code_generators/generate_numpy_api.py
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__multiarray_api.h' to sources.
        executing numpy/core/code_generators/generate_ufunc_api.py
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__ufunc_api.h' to sources.
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath' to include_dirs.
          adding 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/common' to include_dirs.
        numpy.core - nothing done with h_files = ['build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/funcs.inc', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/simd.inc', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/loops.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/matmul.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/clip.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath/npy_math_internal.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/src/common/templ_common.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/config.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/_numpyconfig.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__multiarray_api.h', 'build/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy/__ufunc_api.h']
        building extension "numpy.core._umath_tests" sources
        building extension "numpy.core._rational_tests" sources
        building extension "numpy.core._struct_ufunc_tests" sources
        building extension "numpy.core._operand_flag_tests" sources
        building extension "numpy.fft._pocketfft_internal" sources
        building extension "numpy.linalg.lapack_lite" sources
          adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
        building extension "numpy.linalg._umath_linalg" sources
          adding 'numpy/linalg/lapack_lite/python_xerbla.c' to sources.
        building extension "numpy.random.mt19937" sources
        building extension "numpy.random.philox" sources
        building extension "numpy.random.pcg64" sources
        building extension "numpy.random.sfc64" sources
        building extension "numpy.random.common" sources
        building extension "numpy.random.bit_generator" sources
        building extension "numpy.random.generator" sources
        building extension "numpy.random.bounded_integers" sources
        building extension "numpy.random.mtrand" sources
        building data_files sources
        build_src: building npy-pkg config files
        running build_py
        copying numpy/version.py -> build/lib.macosx-11.0-arm64-cpython-38/numpy
        copying build/src.macosx-11.0-arm64-3.8/numpy/__config__.py -> build/lib.macosx-11.0-arm64-cpython-38/numpy
        copying build/src.macosx-11.0-arm64-3.8/numpy/distutils/__config__.py -> build/lib.macosx-11.0-arm64-cpython-38/numpy/distutils
        running build_clib
        customize UnixCCompiler
        customize UnixCCompiler using build_clib
        running build_ext
        customize UnixCCompiler
        customize UnixCCompiler using build_ext
        building 'numpy.core._multiarray_umath' extension
        compiling C sources
        C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64

        compile options: '-DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/umath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/christersylven/miniforge3/envs/cpdb/include/python3.8 -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -c'
        extra options: '-faltivec -I/System/Library/Frameworks/vecLib.framework/Headers'
        clang: numpy/core/src/multiarray/alloc.cclang: numpy/core/src/multiarray/array_assign_scalar.c

        clang: numpy/core/src/multiarray/buffer.c
        clang: numpy/core/src/multiarray/common.c
        clang: numpy/core/src/multiarray/conversion_utils.c
        clang: numpy/core/src/multiarray/descriptor.c
        clang: numpy/core/src/multiarray/datetime_strings.c
        clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/multiarray/einsum.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/multiarray/hashdescr.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/multiarray/multiarraymodule.c
        clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/multiarray/lowlevel_strided_loops.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/multiarray/nditer_constr.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/multiarray/refcount.c
        clang: numpy/core/src/multiarray/scalarapi.c
        clang: numpy/core/src/multiarray/vdot.c
        clang: numpy/core/src/multiarray/temp_elide.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/loops.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: build/src.macosx-11.0-arm64-3.8/numpy/core/src/umath/scalarmath.cclang: numpy/core/src/umath/ufunc_object.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly

        clang: numpy/core/src/common/npy_longdouble.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/npymath/npy_math.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: numpy/core/src/common/numpyos.c
        clang: /private/var/folders/1g/57wsyq2d1l1__jrtrb0kl3lw0000gn/T/pip-install-o96k_fng/numpy_05d9aa3948644d4b8b6de228dee50d93/numpy/_build_utils/src/apple_sgemv_fix.c
        clang: numpy/core/src/npymath/halffloat.c
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
        error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -fPIC -O2 -isystem /Users/christersylven/miniforge3/envs/cpdb/include -arch arm64 -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/umath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/christersylven/miniforge3/envs/cpdb/include/python3.8 -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/common -Ibuild/src.macosx-11.0-arm64-3.8/numpy/core/src/npymath -c numpy/core/src/multiarray/buffer.c -o build/temp.macosx-11.0-arm64-cpython-38/numpy/core/src/multiarray/buffer.o -MMD -MF build/temp.macosx-11.0-arm64-cpython-38/numpy/core/src/multiarray/buffer.o.d -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: legacy-install-failure

  × Encountered error while trying to install package.
  ╰─> numpy

  note: This is an issue with the package mentioned above, not pip.
  hint: See above for output from the failure.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. (cpdb) @.*** ~ %

14 mars 2023 kl. 19:16 skrev Christer Sylven @.***>:

Thank you so much. I will try that.

14 mars 2023 kl. 19:13 skrev ktroule @.***>:

Sorry for closing this issue. We have a new version of CellPhoneDB which might solve the issues you have pointed to. Read the documentation, and notebooks and try it. Hopefully, this should solve your problems.

— Reply to this email directly, view it on GitHub https://github.com/ventolab/CellphoneDB/issues/76#issuecomment-1468597977, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXFFRBSDOKJTGOQB45XA6LW4CYNDANCNFSM6AAAAAAR5GQXCY. You are receiving this because you commented.

[ktroule]

Hi.

It seems your issue it's related to numpy compilation on the arm architecture. To solve this issue you can try rosetta, please find useful links here and here. Rosetta should translate intel instructions. If you are using conda, make sure that you have installed the right conda installer (ARM version)

The information found in this issue can also be of help.

Kind regards

[chrsyl]

Thank you. With Rosetta it will be run in the intel environment and maybe a bit slow. For the arms environment is seems that the incompatibility is scikit-learn==0.24 that seem to be incompatible and requires a numpy version that also is incompatible. Or am I wrong in these experiences and conclusions? Kind Regards

21 mars 2023 kl. 11:22 skrev ktroule @.***>:

Hi.

It seems your issue it's related to numpy compilation on the arm architecture. To solve this issue you can try rosetta, please find useful links here https://apple.stackexchange.com/questions/409746/run-everything-in-rosetta-2-on-silicon-mac and here https://www.bigbinary.com/books/learn-rubyonrails-book/setting-up-mac. Rosetta should translate intel instructions. If you are using conda, make sure that you have installed the right conda installer (ARM version)

The information found in this https://github.com/numpy/numpy/issues/17807 issue can also be of help.

Kind regards

— Reply to this email directly, view it on GitHub https://github.com/ventolab/CellphoneDB/issues/76#issuecomment-1477587320, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXFFRAHMK36MUREHAXH3A3W5F6PZANCNFSM6AAAAAAR5GQXCY. You are receiving this because you commented.

[chrsyl]

Helo, With the code below I could install cellphonedb in intel environment: ———— base) @. ~ % CONDA_SUBDIR=osx-64 conda create -n cpdb_x86 python=3.8 (base) @. ~ % conda activate cpdb_x86 (cpdb_x86) @. ~ % conda config --env --set subdir osx-64 (cpdb_x86) @. ~ % pip install cellphonedb

---

But it installs cellphonedb 4.0. If I try pip install cellphonedb==4.1.0 I get error. How to install 4.1.0? Kind Regards

22 mars 2023 kl. 19:49 skrev Christer Sylven @.***>:

Thank you. With Rosetta it will be run in the intel environment and maybe a bit slow. For the arms environment is seems that the incompatibility is scikit-learn==0.24 that seem to be incompatible and requires a numpy version that also is incompatible. Or am I wrong in these experiences and conclusions? Kind Regards

21 mars 2023 kl. 11:22 skrev ktroule @.***>:

Hi.

It seems your issue it's related to numpy compilation on the arm architecture. To solve this issue you can try rosetta, please find useful links here https://apple.stackexchange.com/questions/409746/run-everything-in-rosetta-2-on-silicon-mac and here https://www.bigbinary.com/books/learn-rubyonrails-book/setting-up-mac. Rosetta should translate intel instructions. If you are using conda, make sure that you have installed the right conda installer (ARM version)

The information found in this https://github.com/numpy/numpy/issues/17807 issue can also be of help.

Kind regards

— Reply to this email directly, view it on GitHub https://github.com/ventolab/CellphoneDB/issues/76#issuecomment-1477587320, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXFFRAHMK36MUREHAXH3A3W5F6PZANCNFSM6AAAAAAR5GQXCY. You are receiving this because you commented.

[prete]

4.1.0 is the latest release of the database, you can see data releases in the cellphonedb-data repo; the data is accessed via the python package

4.0.0 is the latest version of the python packge; that's what you install if you do pip show cellphonedb you should see "4.0.0" or you can look at the latest release on pypi

[chrsyl]

Helo,According to your doc (please see attached photo) there should be cellphonedb v4.1.0 as well.22 mars 2023 kl. 20:38 skrev Prete @.***>: 4.1.0 is the latest release of the database, you can see data releases in the cellphonedb-data repo; the data is accessed via the python package 4.0.0 is the latest version of the python packge; that's what you install if you do pip show cellphonedb you should see "4.0.0" or you can look at the latest release on pypi

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

[ktroule]

We cannot see the photo, but as @prete has noted the database version is 4.1.0 while the tool version is 4.0.0. If you see indicated the tool as 4.0.1this is an error. Can you indicate where this is so we can correct it.

Thanks

[prete]

@chrsyl images need to be attached on the github issue directly from the web, if you're replying to the emails this won't work. Please use https://github.com/ventolab/CellphoneDB/issues/76 for replying.

[chrsyl]

76 was closed. Here is the link where it is stated release of cellphonedb 4.1.0:

https://cellphonedb.readthedocs.io/en/latest/RESULTS-DOCUMENTATION.html#tutorials

23 mars 2023 kl. 10:30 skrev Prete @.***>:

@chrsyl https://github.com/chrsyl images need to be attached on the github issue directly from the web, if you're replying to the emails this won't work. Please use #76 https://github.com/ventolab/CellphoneDB/issues/76 for replying.

— Reply to this email directly, view it on GitHub https://github.com/ventolab/CellphoneDB/issues/76#issuecomment-1480862071, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABXFFRDXSTAHEUS6GD675M3W5QJ4LANCNFSM6AAAAAAR5GQXCY. You are receiving this because you were mentioned.

[ktroule]

Thanks, we will amend this.