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Pip failed building wheel (MacOS 13, M1 silicon chip) #1883

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Begbo95 opened this issue Dec 20, 2023 · 10 comments
Closed

Pip failed building wheel (MacOS 13, M1 silicon chip) #1883

Begbo95 opened this issue Dec 20, 2023 · 10 comments

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@Begbo95
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Begbo95 commented Dec 20, 2023 •
edited by ihnorton
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Hi all,
I'm unable to install tiledb through pip, possibly due to a similar issue as #710 ?
Pip is able to install 0.10.4 without issues, but I'm trying to install cellxgene_census, which calls for 0.24.0.
Is this an issue or am I doing something wrong? (inexperienced coder here, please be gentle :D)
Grateful for advice :)
Cheers,
Bene

Collecting tiledb==0.24.0
  Using cached tiledb-0.24.0.tar.gz (327 kB)
  Installing build dependencies ... �[?25ldone
etting requirements to build wheel ... �[?25ldone
stalling backend dependencies ... �[?25ldone
g metadata (pyproject.toml) ... �[?25ldone
irement already satisfied: numpy>=1.16.5 in ./opt/anaconda3/lib/python3.9/site-packages (from tiledb==0.24.0) (1.24.3)
Requirement already satisfied: packaging in ./opt/anaconda3/lib/python3.9/site-packages (from tiledb==0.24.0) (23.0)
Building wheels for collected packages: tiledb
  Building wheel for tiledb (pyproject.toml) ... �[?25lerror
  error: subprocess-exited-with-error
  
  × Building wheel for tiledb (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [48 lines of output]
      <string>:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
      TILEDB_PATH from env: ''
      libtiledb_exists checking 'library_dirs': []
      libtiledb_exists found: 'None'
      running bdist_wheel
      xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
      ext_modules:  [<setuptools.extension.Extension('tiledb.libtiledb') at 0x7f7da88a3460>, <setuptools.extension.Extension('tiledb.main') at 0x7f7db8241460>, <pybind11.setup_helpers.Pybind11Extension('tiledb.cc') at 0x7f7da8a5aa60>]
      tiledb_ext:  <setuptools.extension.Extension('tiledb.libtiledb') at 0x7f7da88a3460>
      main_ext:  <setuptools.extension.Extension('tiledb.main') at 0x7f7db8241460>
      tiledb_cc_ext:  <pybind11.setup_helpers.Pybind11Extension('tiledb.cc') at 0x7f7da8a5aa60>
      tiledb_ext.library_dirs:  []
      libtiledb_exists checking 'library_dirs': []
      libtiledb_exists found: 'None'
      Traceback (most recent call last):
        File "/Users/benediktgansen/opt/anaconda3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/benediktgansen/opt/anaconda3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Users/benediktgansen/opt/anaconda3/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in build_wheel
          return self._build_with_temp_dir(
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 389, in _build_with_temp_dir
          self.run_setup()
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 786, in <module>
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command
          super().run_command(command)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-gd6onbtg/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "<string>", line 506, in run
        File "<string>", line 313, in find_or_install_libtiledb
        File "<string>", line 184, in download_libtiledb
        File "/Users/benediktgansen/opt/anaconda3/lib/python3.9/subprocess.py", line 424, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/Users/benediktgansen/opt/anaconda3/lib/python3.9/subprocess.py", line 528, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command '['git', 'clone', '--depth=1', '--branch', '2.18.2', 'https://github.com/TileDB-Inc/TileDB', '/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-install-fk2ncr6w/tiledb_26cbee1a610f465195c75095f3108d12/build/TileDB-2.18.2']' returned non-zero 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 tiledb
ailed to build tiledb
ERROR: Could not build wheels for tiledb, which is required to install pyproject.toml-based projects
Note: you may need to restart the kernel to use updated packages.`
[pip_tiledb_error.txt](https://github.com/TileDB-Inc/TileDB-Py/files/13727708/pip_tiledb_error.txt)
@ihnorton
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ihnorton commented Dec 20, 2023 •
edited
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Hi @Begbo95, we provide wheels for macOS M1 (arm64), so I'm not quite sure why it is trying to build from source (which requires compiler and a few other tools that might not be installed by default).

I just double-checked on my M1 system, in a python 3.9 conda environment:

py39 ❯ pip install tiledb==0.24.0
Collecting tiledb==0.24.0
  Downloading tiledb-0.24.0-cp39-cp39-macosx_11_0_arm64.whl (10.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 7.1 MB/s eta 0:00:00
Requirement already satisfied: numpy>=1.16.5 in /Users/inorton/opt/conda/envs/py39/lib/python3.9/site-packages (from tiledb==0.24.0) (1.23.1)
Requirement already satisfied: packaging in /Users/inorton/opt/conda/envs/py39/lib/python3.9/site-packages (from tiledb==0.24.0) (23.1)
Installing collected packages: tiledb
Successfully installed tiledb-0.24.0

What macOS version are you using?

@Begbo95
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Begbo95 commented Dec 20, 2023

thanks for the quick reply!
I'm using Ventura 13.5.1

@ihnorton
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Ok, I am also on Ventura, and just did the following successfully:

conda create -n cellxgene39
conda activate cellxgene39
conda install "python<3.10" pip
pip install -U cellxgene-census
python

cellxgene39 ❯ python
Python 3.9.18 | packaged by conda-forge | (main, Aug 30 2023, 03:53:08)
[Clang 15.0.7 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cellxgene_census
>>>

Following the cellxgene install instructions here. Could you please try the steps above just to make sure we are on the same page starting from a clean environment?

(Or else, if you are running different install instructions for cellxgene, please link them so I can double-check)

@Begbo95
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Begbo95 commented Dec 20, 2023

sorry for the delay. same issue as before:

(base) ➜  ~ conda activate cellxgene39
(cellxgene39) ➜  ~ conda install "python<3.10" pip
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 23.3.1
  latest version: 23.11.0

Please update conda by running

    $ conda update -n base -c defaults conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.11.0



## Package Plan ##

  environment location: /Users/benediktgansen/opt/anaconda3/envs/cellxgene39

  added / updated specs:
    - pip
    - python[version='<3.10']


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    openssl-3.0.12             |       hca72f7f_0         4.5 MB
    python-3.9.18              |       h5ee71fb_0        12.7 MB
    xz-5.4.5                   |       h6c40b1e_0         366 KB
    ------------------------------------------------------------
                                           Total:        17.6 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2023.12.12-hecd8cb5_0 
  libcxx             pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 
  libffi             pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_0 
  ncurses            pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 
  openssl            pkgs/main/osx-64::openssl-3.0.12-hca72f7f_0 
  pip                pkgs/main/osx-64::pip-23.3.1-py39hecd8cb5_0 
  python             pkgs/main/osx-64::python-3.9.18-h5ee71fb_0 
  readline           pkgs/main/osx-64::readline-8.2-hca72f7f_0 
  setuptools         pkgs/main/osx-64::setuptools-68.2.2-py39hecd8cb5_0 
  sqlite             pkgs/main/osx-64::sqlite-3.41.2-h6c40b1e_0 
  tk                 pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0 
  tzdata             pkgs/main/noarch::tzdata-2023c-h04d1e81_0 
  wheel              pkgs/main/osx-64::wheel-0.41.2-py39hecd8cb5_0 
  xz                 pkgs/main/osx-64::xz-5.4.5-h6c40b1e_0 
  zlib               pkgs/main/osx-64::zlib-1.2.13-h4dc903c_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages
                                                                                
Preparing transaction: done                                                     
Verifying transaction: done                                                     
Executing transaction: done
(cellxgene39) ➜  ~ pip install -U cellxgene-census
python

Collecting cellxgene-census
  Downloading cellxgene_census-1.9.1-py3-none-any.whl.metadata (2.4 kB)
Collecting tiledbsoma~=1.6.0 (from cellxgene-census)
  Downloading tiledbsoma-1.6.1-cp39-cp39-macosx_10_14_x86_64.whl.metadata (5.2 kB)
Collecting anndata (from cellxgene-census)
  Downloading anndata-0.10.3-py3-none-any.whl.metadata (6.4 kB)
Collecting numpy<1.25,>=1.21 (from cellxgene-census)
  Downloading numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (5.6 kB)
Collecting requests (from cellxgene-census)
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting typing-extensions (from cellxgene-census)
  Downloading typing_extensions-4.9.0-py3-none-any.whl.metadata (3.0 kB)
Collecting s3fs>=2021.06.1 (from cellxgene-census)
  Downloading s3fs-2023.12.2-py3-none-any.whl.metadata (1.6 kB)
Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs>=2021.06.1->cellxgene-census)
  Downloading aiobotocore-2.9.0-py3-none-any.whl.metadata (20 kB)
Collecting fsspec==2023.12.2 (from s3fs>=2021.06.1->cellxgene-census)
  Downloading fsspec-2023.12.2-py3-none-any.whl.metadata (6.8 kB)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from s3fs>=2021.06.1->cellxgene-census)
  Downloading aiohttp-3.9.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (7.4 kB)
Collecting attrs>=22.2 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 3.8 MB/s eta 0:00:00
Collecting pandas (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading pandas-2.1.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (18 kB)
Collecting pyarrow-hotfix (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading pyarrow_hotfix-0.6-py3-none-any.whl.metadata (3.6 kB)
Collecting scanpy>=1.9.2 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading scanpy-1.9.6-py3-none-any.whl.metadata (6.0 kB)
Collecting scipy (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading scipy-1.11.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 5.4 MB/s eta 0:00:00
Collecting somacore==1.0.6 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading somacore-1.0.6-py3-none-any.whl.metadata (1.5 kB)
Collecting tiledb~=0.24.0 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading tiledb-0.24.0.tar.gz (327 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 327.2/327.2 kB 18.0 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pyarrow<13.0.0,>=9.0.0 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading pyarrow-12.0.1-cp39-cp39-macosx_10_14_x86_64.whl.metadata (3.0 kB)
Collecting numba==0.56.4 (from tiledbsoma~=1.6.0->cellxgene-census)
  Downloading numba-0.56.4-cp39-cp39-macosx_10_14_x86_64.whl (2.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 39.0 MB/s eta 0:00:00
Collecting numpy<1.25,>=1.21 (from cellxgene-census)
  Downloading numpy-1.23.5-cp39-cp39-macosx_10_9_x86_64.whl (18.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.1/18.1 MB 49.7 MB/s eta 0:00:00
Collecting llvmlite<0.40,>=0.39.0dev0 (from numba==0.56.4->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading llvmlite-0.39.1-cp39-cp39-macosx_10_9_x86_64.whl (25.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 25.5/25.5 MB 35.4 MB/s eta 0:00:00
Requirement already satisfied: setuptools in ./opt/anaconda3/envs/cellxgene39/lib/python3.9/site-packages (from numba==0.56.4->tiledbsoma~=1.6.0->cellxgene-census) (68.2.2)
Collecting array-api-compat (from anndata->cellxgene-census)
  Downloading array_api_compat-1.4-py3-none-any.whl.metadata (13 kB)
Collecting exceptiongroup (from anndata->cellxgene-census)
  Using cached exceptiongroup-1.2.0-py3-none-any.whl.metadata (6.6 kB)
Collecting h5py>=3 (from anndata->cellxgene-census)
  Downloading h5py-3.10.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB)
Collecting natsort (from anndata->cellxgene-census)
  Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting packaging>=20 (from anndata->cellxgene-census)
  Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting charset-normalizer<4,>=2 (from requests->cellxgene-census)
  Downloading charset_normalizer-3.3.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->cellxgene-census)
  Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests->cellxgene-census)
  Downloading urllib3-2.1.0-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests->cellxgene-census)
  Downloading certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB)
Collecting botocore<1.33.14,>=1.33.2 (from aiobotocore<3.0.0,>=2.5.4->s3fs>=2021.06.1->cellxgene-census)
  Downloading botocore-1.33.13-py3-none-any.whl.metadata (6.1 kB)
Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs>=2021.06.1->cellxgene-census)
  Downloading wrapt-1.16.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (6.6 kB)
Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs>=2021.06.1->cellxgene-census)
  Downloading aioitertools-0.11.0-py3-none-any.whl (23 kB)
Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->s3fs>=2021.06.1->cellxgene-census)
  Downloading multidict-6.0.4-cp39-cp39-macosx_10_9_x86_64.whl (29 kB)
Collecting yarl<2.0,>=1.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->s3fs>=2021.06.1->cellxgene-census)
  Downloading yarl-1.9.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (31 kB)
Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->s3fs>=2021.06.1->cellxgene-census)
  Downloading frozenlist-1.4.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (12 kB)
Collecting aiosignal>=1.1.2 (from aiohttp!=4.0.0a0,!=4.0.0a1->s3fs>=2021.06.1->cellxgene-census)
  Downloading aiosignal-1.3.1-py3-none-any.whl (7.6 kB)
Collecting async-timeout<5.0,>=4.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->s3fs>=2021.06.1->cellxgene-census)
  Downloading async_timeout-4.0.3-py3-none-any.whl.metadata (4.2 kB)
Collecting python-dateutil>=2.8.2 (from pandas->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 22.6 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.1 (from pandas->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.8/341.8 kB 31.1 MB/s eta 0:00:00
Collecting get-annotations (from scanpy>=1.9.2->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading get_annotations-0.1.2-py3-none-any.whl (4.5 kB)
Collecting joblib (from scanpy>=1.9.2->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting matplotlib>=3.4 (from scanpy>=1.9.2->tiledbsoma~=1.6.0->cellxgene-census)
  Downloading matplotlib-3.8.2-cp39-cp39-macosx_10_12_x86_64.whl.metadata (5.8 kB)
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Building wheels for collected packages: tiledb
  Building wheel for tiledb (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for tiledb (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [48 lines of output]
      <string>:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
      WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section'
      TILEDB_PATH from env: ''
      libtiledb_exists checking 'library_dirs': []
      libtiledb_exists found: 'None'
      running bdist_wheel
      xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
      ext_modules:  [<setuptools.extension.Extension('tiledb.libtiledb') at 0x7fe9e06e6a60>, <setuptools.extension.Extension('tiledb.main') at 0x7fe9d019fa60>, <pybind11.setup_helpers.Pybind11Extension('tiledb.cc') at 0x7fe9e083b3a0>]
      tiledb_ext:  <setuptools.extension.Extension('tiledb.libtiledb') at 0x7fe9e06e6a60>
      main_ext:  <setuptools.extension.Extension('tiledb.main') at 0x7fe9d019fa60>
      tiledb_cc_ext:  <pybind11.setup_helpers.Pybind11Extension('tiledb.cc') at 0x7fe9e083b3a0>
      tiledb_ext.library_dirs:  []
      libtiledb_exists checking 'library_dirs': []
      libtiledb_exists found: 'None'
      Traceback (most recent call last):
        File "/Users/benediktgansen/opt/anaconda3/envs/cellxgene39/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/benediktgansen/opt/anaconda3/envs/cellxgene39/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Users/benediktgansen/opt/anaconda3/envs/cellxgene39/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in build_wheel
          return self._build_with_temp_dir(
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 389, in _build_with_temp_dir
          self.run_setup()
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup
          exec(code, locals())
        File "<string>", line 786, in <module>
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command
          super().run_command(command)
        File "/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-build-env-bibmj1t_/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "<string>", line 506, in run
        File "<string>", line 313, in find_or_install_libtiledb
        File "<string>", line 184, in download_libtiledb
        File "/Users/benediktgansen/opt/anaconda3/envs/cellxgene39/lib/python3.9/subprocess.py", line 424, in check_output
          return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
        File "/Users/benediktgansen/opt/anaconda3/envs/cellxgene39/lib/python3.9/subprocess.py", line 528, in run
          raise CalledProcessError(retcode, process.args,
      subprocess.CalledProcessError: Command '['git', 'clone', '--depth=1', '--branch', '2.18.2', 'https://github.com/TileDB-Inc/TileDB', '/private/var/folders/yt/7clzs2dj42n_69mbbsh6tvg80000gn/T/pip-install-yn6i3s3n/tiledb_8f4fd525b39647b1bad3a4af492df92c/build/TileDB-2.18.2']' returned non-zero 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 tiledb
Failed to build tiledb
ERROR: Could not build wheels for tiledb, which is required to install pyproject.toml-based projects
Python 3.9.18 (main, Sep 11 2023, 08:38:23) 
[Clang 14.0.6 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 
>>>

@ihnorton
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Ok, it looks like your conda environment is defaulting to osx-64 (intel) rather than arm64 (M1). That should still work, and it does work for me -- but let's try with arm64 instead.

export CONDA_SUBDIR=osx-arm64
conda create -n cellxgene39 "python<3.9" pip
conda activate cellxgene39
conda config --env --set subdir osx-arm64
pip install -U cellxgene-census

(x-ref https://stackoverflow.com/a/65432861/508431)

@Begbo95
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Begbo95 commented Dec 20, 2023

this ran beautifully :) thanks a lot for your time and help! can i force the arm64 in base, or is that not advised? i like to run Spyder IDE in base (through anaconda) for exploratory data analysis, where envs are a bit finnicky (or at least I'm not well enough trained)

@ihnorton
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I would probably reinstall conda with the arm64/m1 installer, to be honest... I would be surprised if it is possible to update base to a different architecture in-place. It should be possible to do this without losing your existing environments, although I couldn't immediately find any step-by-step instructions for migrating. Just to be safe, you might want to export your existing environments so that they can be recreated.

@ihnorton
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I'll close this for now, happy to reopen if needed in the future.

@Begbo95
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Begbo95 commented Dec 20, 2023

amazing, thanks again!
cheers from Germany :)

@Begbo95
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Begbo95 commented Dec 21, 2023 •
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a little update: I managed to get it installed in base using SYSTEM_VERSION_COMPAT=0
the background is that i tried to install gget in the cellxgene39 env, but got the exact opposite issue: pip installed it fine in base, but not cellxgene39. However, gget relies on cellxgene-census, so i needed both in the same env.
Might be a python issue on old MacOS PDK that's not been solven in pip yet (according to xref: microsoft/onnxruntime#17166 )
Not sure how to fix it, but this workaround works for me so far.

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