Numpy import error when using conda-forge build of numpy 2.2.3 // no issue with pip

[bakj1979]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Problem
Started getting import error for numpy in existing environment earlier this week after conda update -all, so I wiped everything and now have a clean install of Sequoia and miniforge (where I followed instructions from README).

I have created a new conda env and installed python 3.12 and numpy using conda-forge distrib, and it gives me the same import error. When I remove numpy and reinstall with pip, I do not get any problems. It does require me to then install all apps that have dependencies on numpy (e.g. pandas or matplotlib) with pip, as it is other wise (re)installed using conda-forge as its source.

Conda was installed with standalone installer my MBP M4 Max running MacOS 15.3.

Error upon numpy import:

 Traceback (most recent call last):
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/overrides.py", line 7, in <module>
    from numpy._core._multiarray_umath import (
ImportError: dlopen(/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <CAA510D4-816A-34E5-9021-485EF5D56159> /Users/jeffreybaker/miniforge3/envs/test-env/lib/libopenblas.0.dylib
  Reason: tried: '/Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/__init__.py", line 114, in <module>
    from numpy.__config__ import show_config
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy._core._multiarray_umath import (
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.12 from "/Users/jeffreybaker/miniforge3/envs/test-env/bin/python"
  * The NumPy version is: "2.2.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <CAA510D4-816A-34E5-9021-485EF5D56159> /Users/jeffreybaker/miniforge3/envs/test-env/lib/libopenblas.0.dylib
  Reason: tried: '/Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/test-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/jeffreybaker/miniforge3/envs/test-env/lib/python3.12/site-packages/numpy/__init__.py", line 119, in <module>
    raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Installed packages

**Packages when everything installed through conda-forge:**
bzip2                     1.0.8                h99b78c6_7    conda-forge
ca-certificates           2025.1.31            hf0a4a13_0    conda-forge
libblas                   3.9.0           31_h10e41b3_openblas    conda-forge
libcblas                  3.9.0           31_hb3479ef_openblas    conda-forge
libcxx                    19.1.7               ha82da77_0    conda-forge
libexpat                  2.6.4                h286801f_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
liblapack                 3.9.0           31_hc9a63f6_openblas    conda-forge
liblzma                   5.6.4                h39f12f2_0    conda-forge
libopenblas               0.3.29          openmp_hf332438_0    conda-forge
libsqlite                 3.49.1               h3f77e49_1    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
llvm-openmp               19.1.7               hdb05f8b_0    conda-forge
ncurses                   6.5                  h5e97a16_3    conda-forge
numpy                     2.2.3           py312h7c1f314_0    conda-forge
openssl                   3.4.1                h81ee809_0    conda-forge
pip                       25.0.1             pyh8b19718_0    conda-forge
python                    3.12.9          hc22306f_0_cpython    conda-forge
python_abi                3.12                    5_cp312    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
setuptools                75.8.0             pyhff2d567_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tzdata                    2025a                h78e105d_0    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge

**Packages where numpy sourced from pip:**

# packages in environment at /Users/jeffreybaker/miniforge3/envs/spyder-env:
#
# Name                    Version                   Build  Channel
aiohappyeyeballs          2.4.6              pyhd8ed1ab_0    conda-forge
aiohttp                   3.11.12         py312h998013c_0    conda-forge
aiosignal                 1.3.2              pyhd8ed1ab_0    conda-forge
alabaster                 1.0.0              pyhd8ed1ab_1    conda-forge
applaunchservices         0.3.0              pyh534df25_4    conda-forge
appnope                   0.1.4              pyhd8ed1ab_1    conda-forge
arrow                     1.3.0              pyhd8ed1ab_1    conda-forge
astroid                   3.3.8           py312h81bd7bf_0    conda-forge
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
asyncssh                  2.20.0             pyhd8ed1ab_0    conda-forge
atomicwrites              1.4.1              pyhd8ed1ab_1    conda-forge
attrs                     25.1.0             pyh71513ae_0    conda-forge
autopep8                  2.0.4              pyhd8ed1ab_0    conda-forge
babel                     2.17.0             pyhd8ed1ab_0    conda-forge
backports                 1.0                pyhd8ed1ab_5    conda-forge
backports.tarfile         1.2.0              pyhd8ed1ab_1    conda-forge
beautifulsoup4            4.13.3             pyha770c72_0    conda-forge
binaryornot               0.4.4              pyhd8ed1ab_2    conda-forge
black                     25.1.0          py312h81bd7bf_0    conda-forge
bleach                    6.2.0              pyh29332c3_4    conda-forge
bleach-with-css           6.2.0                h82add2a_4    conda-forge
brotli-python             1.1.0           py312hde4cb15_2    conda-forge
bzip2                     1.0.8                h99b78c6_7    conda-forge
ca-certificates           2025.1.31            hf0a4a13_0    conda-forge
certifi                   2025.1.31          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312h0fad829_0    conda-forge
chardet                   5.2.0           py312h81bd7bf_2    conda-forge
charset-normalizer        3.4.1              pyhd8ed1ab_0    conda-forge
click                     8.1.8              pyh707e725_0    conda-forge
cloudpickle               3.1.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
comm                      0.2.2              pyhd8ed1ab_1    conda-forge
cookiecutter              2.6.0              pyhd8ed1ab_1    conda-forge
cryptography              44.0.1          py312hf9bd80e_0    conda-forge
cyrus-sasl                2.1.27               h60b93bd_7    conda-forge
debugpy                   1.8.12          py312hd8f9ff3_0    conda-forge
decorator                 5.2.0              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.18             pyhd8ed1ab_0    conda-forge
diff-match-patch          20241021           pyhd8ed1ab_1    conda-forge
dill                      0.3.9              pyhd8ed1ab_1    conda-forge
docstring-to-markdown     0.15               pyhd8ed1ab_1    conda-forge
docutils                  0.21.2             pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
flake8                    7.1.2              pyhd8ed1ab_0    conda-forge
frozenlist                1.5.0           py312h998013c_1    conda-forge
fzf                       0.60.1               h8842463_0    conda-forge
giflib                    5.2.2                h93a5062_0    conda-forge
glib                      2.82.2               heee381b_1    conda-forge
glib-tools                2.82.2               h1dc7a0c_1    conda-forge
gst-plugins-base          1.24.7               hb49d354_0    conda-forge
gstreamer                 1.24.7               hc3f5269_0    conda-forge
h2                        4.2.0              pyhd8ed1ab_0    conda-forge
hpack                     4.1.0              pyhd8ed1ab_0    conda-forge
hyperframe                6.1.0              pyhd8ed1ab_0    conda-forge
icu                       75.1                 hfee45f7_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        8.6.1              pyha770c72_0    conda-forge
importlib_resources       6.5.2              pyhd8ed1ab_0    conda-forge
inflection                0.5.1              pyhd8ed1ab_1    conda-forge
intervaltree              3.1.0              pyhd8ed1ab_1    conda-forge
ipykernel                 6.29.5             pyh57ce528_0    conda-forge
ipython                   8.32.0             pyh907856f_0    conda-forge
isort                     6.0.0              pyhd8ed1ab_0    conda-forge
jaraco.classes            3.4.0              pyhd8ed1ab_2    conda-forge
jaraco.context            6.0.1              pyhd8ed1ab_0    conda-forge
jaraco.functools          4.1.0              pyhd8ed1ab_0    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
jellyfish                 1.1.3           py312hcd83bfe_0    conda-forge
jinja2                    3.1.5              pyhd8ed1ab_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_1    conda-forge
jupyter_client            8.6.3              pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_2    conda-forge
keyring                   25.6.0             pyh534df25_0    conda-forge
krb5                      1.21.3               h237132a_0    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libclang-cpp17            17.0.6          default_hf90f093_8    conda-forge
libclang13                19.1.7          default_h81d93ff_1    conda-forge
libcxx                    19.1.7               ha82da77_0    conda-forge
libdeflate                1.23                 hec38601_0    conda-forge
libedit                   3.1.20250104    pl5321hafb1f1b_0    conda-forge
libexpat                  2.6.4                h286801f_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libglib                   2.82.2               hdff4504_1    conda-forge
libiconv                  1.18                 hfe07756_1    conda-forge
libintl                   0.23.1               h493aca8_0    conda-forge
libintl-devel             0.23.1               h493aca8_0    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
libllvm17                 17.0.6               hc4b4ae8_3    conda-forge
libllvm19                 19.1.7               hc4b4ae8_1    conda-forge
liblzma                   5.6.4                h39f12f2_0    conda-forge
libntlm                   1.8                  h5505292_0    conda-forge
libogg                    1.3.5                h99b78c6_0    conda-forge
libopus                   1.3.1                h27ca646_1    conda-forge
libpng                    1.6.47               h3783ad8_0    conda-forge
libpq                     17.4                 h6896619_0    conda-forge
libsodium                 1.0.20               h99b78c6_0    conda-forge
libspatialindex           2.1.0                h57eeb1c_0    conda-forge
libsqlite                 3.49.1               h3f77e49_1    conda-forge
libtiff                   4.7.0                h551f018_3    conda-forge
libvorbis                 1.3.7                h9f76cd9_0    conda-forge
libwebp                   1.5.0                h1618228_0    conda-forge
libwebp-base              1.5.0                h2471fea_0    conda-forge
libxml2                   2.13.6               h178c5d8_0    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_1    conda-forge
markupsafe                3.0.2           py312h998013c_1    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_1    conda-forge
mccabe                    0.7.0              pyhd8ed1ab_1    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_1    conda-forge
mistune                   3.1.2              pyhd8ed1ab_0    conda-forge
more-itertools            10.6.0             pyhd8ed1ab_0    conda-forge
multidict                 6.1.0           py312hdb8e49c_1    conda-forge
mypy_extensions           1.0.0              pyha770c72_1    conda-forge
mysql-common              9.0.1                hd7719f6_4    conda-forge
mysql-libs                9.0.1                ha8be5b7_4    conda-forge
nbclient                  0.10.2             pyhd8ed1ab_0    conda-forge
nbconvert                 7.16.6               hb482800_0    conda-forge
nbconvert-core            7.16.6             pyh29332c3_0    conda-forge
nbconvert-pandoc          7.16.6               hed9df3c_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_1    conda-forge
ncurses                   6.5                  h5e97a16_3    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_1    conda-forge
nspr                      4.36                 h5833ebf_0    conda-forge
nss                       3.108                ha3c76ea_0    conda-forge
numpy                     2.2.3                    pypi_0    pypi
numpydoc                  1.8.0              pyhd8ed1ab_1    conda-forge
openldap                  2.6.9                hbe55e7a_0    conda-forge
openssl                   3.4.1                h81ee809_0    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
pandas                    2.2.3                    pypi_0    pypi
pandoc                    3.6.3                hce30654_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_1    conda-forge
pathspec                  0.12.1             pyhd8ed1ab_1    conda-forge
pcre2                     10.44                h297a79d_2    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pickleshare               0.7.5           pyhd8ed1ab_1004    conda-forge
pip                       25.0.1             pyh8b19718_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_2    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_1    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_1    conda-forge
ply                       3.11               pyhd8ed1ab_3    conda-forge
prompt-toolkit            3.0.50             pyha770c72_0    conda-forge
propcache                 0.2.1           py312h998013c_1    conda-forge
psutil                    6.1.1           py312hea69d52_0    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pycodestyle               2.12.1             pyhd8ed1ab_1    conda-forge
pyconify                  0.2.1              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pydocstyle                6.3.0              pyhd8ed1ab_1    conda-forge
pyflakes                  3.2.0              pyhd8ed1ab_1    conda-forge
pygithub                  2.6.1              pyhd8ed1ab_0    conda-forge
pygments                  2.19.1             pyhd8ed1ab_0    conda-forge
pyjwt                     2.10.1             pyhd8ed1ab_0    conda-forge
pylint                    3.3.4              pyh29332c3_0    conda-forge
pylint-venv               3.0.4              pyhd8ed1ab_1    conda-forge
pyls-spyder               0.4.0              pyhd8ed1ab_1    conda-forge
pynacl                    1.5.0           py312h024a12e_4    conda-forge
pyobjc-core               11.0            py312hb9d441b_0    conda-forge
pyobjc-framework-cocoa    11.0            py312hb9d441b_0    conda-forge
pyobjc-framework-coreservices 11.0            py312hea69d52_0    conda-forge
pyobjc-framework-fsevents 11.0            py312h81bd7bf_0    conda-forge
pyopenssl                 25.0.0             pyhd8ed1ab_0    conda-forge
pyqt                      5.15.9          py312h550cae4_5    conda-forge
pyqt5-sip                 12.12.2         py312h9f69965_5    conda-forge
pyqtwebengine             5.15.9          py312h14105d7_5    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.12.9          hc22306f_0_cpython    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-fastjsonschema     2.21.1             pyhd8ed1ab_0    conda-forge
python-gssapi             1.9.0           py312h97903a5_1    conda-forge
python-lsp-black          2.0.0              pyhff2d567_1    conda-forge
python-lsp-jsonrpc        1.1.2              pyhff2d567_1    conda-forge
python-lsp-server         1.12.2             pyhff2d567_0    conda-forge
python-lsp-server-base    1.12.2             pyhd8ed1ab_0    conda-forge
python-slugify            8.0.4              pyhd8ed1ab_1    conda-forge
python.app                1.4             py312h830b0dc_4    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pytoolconfig              1.2.5              pyhd8ed1ab_1    conda-forge
pytz                      2025.1             pyhd8ed1ab_0    conda-forge
pyuca                     1.2                pyhd8ed1ab_2    conda-forge
pyxdg                     0.28               pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2           py312h998013c_2    conda-forge
pyzmq                     26.2.1          py312hf4875e0_0    conda-forge
qdarkstyle                3.2.3              pyhd8ed1ab_1    conda-forge
qstylizer                 0.2.4              pyhff2d567_0    conda-forge
qt-main                   5.15.15              h67564f6_2    conda-forge
qt-webengine              5.15.15              h5422c0a_1    conda-forge
qtawesome                 1.3.1              pyh9208f05_1    conda-forge
qtconsole                 5.6.1              pyhd8ed1ab_1    conda-forge
qtconsole-base            5.6.1              pyha770c72_1    conda-forge
qtpy                      2.4.3              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
referencing               0.36.2             pyh29332c3_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
rich                      13.9.4             pyhd8ed1ab_1    conda-forge
roman-numerals-py         3.1.0              pyhd8ed1ab_0    conda-forge
rope                      1.13.0             pyhd8ed1ab_1    conda-forge
rpds-py                   0.23.1          py312hd60eec9_0    conda-forge
rtree                     1.3.0           py312hda3fc1a_3    conda-forge
setuptools                75.8.0             pyhff2d567_0    conda-forge
sip                       6.8.6           py312hde4cb15_1    conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_1    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    8.2.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-devhelp     2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-htmlhelp    2.1.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_1    conda-forge
sphinxcontrib-qthelp      2.0.0              pyhd8ed1ab_1    conda-forge
sphinxcontrib-serializinghtml 1.1.10             pyhd8ed1ab_1    conda-forge
spyder                    6.0.4                hd8ed1ab_1    conda-forge
spyder-base               6.0.4           osx_pyh1a5313d_1    conda-forge
spyder-kernels            3.0.3           unix_pyh707e725_0    conda-forge
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
superqt                   0.7.0              pyhb6d5dde_0    conda-forge
tabulate                  0.9.0              pyhd8ed1ab_2    conda-forge
text-unidecode            1.3                pyhd8ed1ab_2    conda-forge
textdistance              4.6.3              pyhd8ed1ab_1    conda-forge
three-merge               0.1.1              pyhd8ed1ab_1    conda-forge
tinycss2                  1.4.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_1    conda-forge
tomli                     2.2.1              pyhd8ed1ab_1    conda-forge
tomlkit                   0.13.2             pyha770c72_1    conda-forge
tornado                   6.4.2           py312hea69d52_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
types-python-dateutil     2.9.0.20241206     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
tzdata                    2025.1                   pypi_0    pypi
ujson                     5.10.0          py312hde4cb15_1    conda-forge
urllib3                   2.3.0              pyhd8ed1ab_0    conda-forge
watchdog                  6.0.0           py312hea69d52_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
webencodings              0.5.1              pyhd8ed1ab_3    conda-forge
whatthepatch              1.0.7              pyhd8ed1ab_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
wrapt                     1.17.2          py312hea69d52_0    conda-forge
wurlitzer                 3.1.1              pyhd8ed1ab_1    conda-forge
yaml                      0.2.5                h3422bc3_2    conda-forge
yapf                      0.43.0             pyhd8ed1ab_1    conda-forge
yarl                      1.18.3          py312h998013c_1    conda-forge
zeromq                    4.3.5                hc1bb282_7    conda-forge
zipp                      3.21.0             pyhd8ed1ab_1    conda-forge
zstandard                 0.23.0          py312h15fbf35_1    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

Environment info

active environment : base
    active env location : /Users/jeffreybaker/miniforge3
            shell level : 1
       user config file : /Users/jeffreybaker/.condarc
 populated config files : /Users/jeffreybaker/miniforge3/.condarc
          conda version : 25.1.1
    conda-build version : not installed
         python version : 3.13.2.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=m1
                          __conda=25.1.1=0
                          __osx=15.4=0
                          __unix=0=0
       base environment : /Users/jeffreybaker/miniforge3  (writable)
      conda av data dir : /Users/jeffreybaker/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/jeffreybaker/miniforge3/pkgs
                          /Users/jeffreybaker/.conda/pkgs
       envs directories : /Users/jeffreybaker/miniforge3/envs
                          /Users/jeffreybaker/.conda/envs
               platform : osx-arm64
             user-agent : conda/25.1.1 requests/2.32.3 CPython/3.13.2 Darwin/24.4.0 OSX/15.4 solver/libmamba conda-libmamba-solver/25.1.1 libmambapy/2.0.5
                UID:GID : 501:20
             netrc file : None
           offline mode : False

[h-vetinari]

Thanks for the issue. Can you please provide the result of

otool -l /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib | grep -A2 LC_RPATH

[bakj1979]

sure np:

(test-env) jeffreybaker@Js-MB-Pro-M4-Max ~ % otool -l /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib | grep -A2 LC_RPATH
—
          cmd LC_RPATH
      cmdsize 32
         path @loader_path (offset 12)
--
          cmd LC_RPATH
      cmdsize 32
         path @loader_path (offset 12)
--
          cmd LC_RPATH
      cmdsize 32
         path @loader_path/ (offset 12)
zsh: command not found: —

[h-vetinari]

Can you do

install_name_tool -delete_rpath @loader_path /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib
install_name_tool -delete_rpath @loader_path/ /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib
install_name_tool -add_rpath @loader_path /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

and then try again?

Also, please wrap outputs of logs/traces etc. in triple-backticks. I've edited your posts to this effect.

[bakj1979]

Hello, I get the following when I run that in terminal in my conda base when running those three lines. ``` error: /Library/Developer/CommandLineTools/usr/bin/install_name_tool: no LC_RPATH load command with path: @loader_path found in: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib (for architecture arm64), required for specified option "-delete_rpath @loader_path" error: /Library/Developer/CommandLineTools/usr/bin/install_name_tool: no LC_RPATH load command with path: @loader_path/ found in: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib (for architecture arm64), required for specified option "-delete_rpath @loader_path/“ /Library/Developer/CommandLineTools/usr/bin/install_name_tool: warning: changes being made to the file will invalidate the code signature in: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib ``` Thank you

[h-vetinari]

This is a backtick: `

You need three of them before/after your code blocks.

You can try with quoting

install_name_tool -delete_rpath "@loader_path" /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib
install_name_tool -delete_rpath "@loader_path/" /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib
install_name_tool -add_rpath "@loader_path" /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

after ensuring that the file is writeable, e.g.

chmod +w /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Otherwise I'm out of ideas here.

[bakj1979]

Apologies, I mistakenly read "brackets".

so I've uninstalled conda/miniforge and reinstalled and have noticed an unexpected error once I have indicated that I want to automatically initialise conda, I get the block set out below. Why is it referencing mamba and why would there be an error in a new install?

To activate this environment, use:

    micromamba activate /Users/jeffreybaker/miniforge3

Or to execute a single command in this environment, use:

    micromamba run -p /Users/jeffreybaker/miniforge3 mycommand

installation finished.
Do you wish to update your shell profile to automatically initialize conda?
This will activate conda on startup and change the command prompt when activated.
If you'd prefer that conda's base environment not be activated on startup,
   run the following command when conda is activated:

conda config --set auto_activate_base false

You can undo this by running `conda init --reverse $SHELL`? [yes|no]
[no] >>> yes
no change     /Users/jeffreybaker/miniforge3/condabin/conda
no change     /Users/jeffreybaker/miniforge3/bin/conda
no change     /Users/jeffreybaker/miniforge3/bin/conda-env
no change     /Users/jeffreybaker/miniforge3/bin/activate
no change     /Users/jeffreybaker/miniforge3/bin/deactivate
no change     /Users/jeffreybaker/miniforge3/etc/profile.d/conda.sh
no change     /Users/jeffreybaker/miniforge3/etc/fish/conf.d/conda.fish
no change     /Users/jeffreybaker/miniforge3/shell/condabin/Conda.psm1
no change     /Users/jeffreybaker/miniforge3/shell/condabin/conda-hook.ps1
no change     /Users/jeffreybaker/miniforge3/lib/python3.12/site-packages/xontrib/conda.xsh
no change     /Users/jeffreybaker/miniforge3/etc/profile.d/conda.csh
no change     /Users/jeffreybaker/.zshrc
No action taken.
/Users/jeffreybaker/Desktop/Miniforge3-MacOSX-arm64.sh: line 479: [: 1
24: integer expression expected
usage: mamba [-h] [-v] [--no-plugins] [-V] COMMAND ...
mamba: error: argument COMMAND: invalid choice: 'shell' (choose from activate, clean, commands, compare, config, create, deactivate, env, export, info, init, install, list, notices, package, doctor, repoquery, remove, uninstall, rename, run, search, update, upgrade)

[h-vetinari]

This is a triple backtick: ```. This triple backtick needs to become both before and after a block of lines that should be formatted like a log.

If this is still unclear, I want you to click "edit" on one of your posts and see for yourself how I've modified it. Further, you should use the "Preview" button when writing (or editing) a comment to check that it is formatted correctly. I will stop responding if you cannot handle this basic bit of etiquette after 3 separate explanations.

so I've uninstalled conda/miniforge and reinstalled and have noticed an unexpected error once I have indicated that I want to automatically initialise conda, I get the block set out below. Why is it referencing mamba and why would there be an error in a new install?

Uninstalling conda/micromamba will not change this, though of course you should check that your installer is up to date. The error you showed is unrelated to the issue here.

[bakj1979]

Apologies. You might have noticed that I did indeed include backticks but was unaware that it was not on a new line. My goal is to solve the problem, not offend a mod.

I have created a new environment, installed the (very few packages) I need for my model and have re-ran the instructions you kindly provided.

The first instruction:

otool -l /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib | grep -A2 LC_RPATH

returns:

          cmd LC_RPATH
      cmdsize 32
         path @loader_path (offset 12)
--
          cmd LC_RPATH
      cmdsize 32
         path @loader_path (offset 12)
--
          cmd LC_RPATH
      cmdsize 32
         path @loader_path/ (offset 12)

and your further instructions return:

Instruction 1:

install_name_tool -delete_rpath "@loader_path" /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Return 1:

/Library/Developer/CommandLineTools/usr/bin/install_name_tool: warning: changes being made to the file will invalidate the code signature in: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Instruction 2:

install_name_tool -delete_rpath @loader_path/ /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Return 2:

/Library/Developer/CommandLineTools/usr/bin/install_name_tool: warning: changes being made to the file will invalidate the code signature in: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Instruction 3

install_name_tool -add_rpath "@loader_path" /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib

Return 3:

error: /Library/Developer/CommandLineTools/usr/bin/install_name_tool: for: /Users/jeffreybaker/miniforge3/envs/test-env/lib/libgfortran.5.dylib (for architecture arm64) option "-add_rpath @loader_path" would duplicate path, file already has LC_RPATH for: @loader_path

And now when I activate the test-env environment, Spyder crashes, so created a new environment with just python 3.12, ipython, numpy, but unfortunately still have the same error despite libgfortran and libgfortran.5 being installed (see below).

Package List:

# packages in environment at /Users/jeffreybaker/miniforge3/envs/spyder-env:
#
# Name                    Version                   Build  Channel
asttokens                 3.0.0              pyhd8ed1ab_1    conda-forge
bzip2                     1.0.8                h99b78c6_7    conda-forge
ca-certificates           2025.1.31            hf0a4a13_0    conda-forge
decorator                 5.2.1              pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
executing                 2.1.0              pyhd8ed1ab_1    conda-forge
ipython                   8.32.0             pyh907856f_0    conda-forge
jedi                      0.19.2             pyhd8ed1ab_1    conda-forge
libblas                   3.9.0           31_h10e41b3_openblas    conda-forge
libcblas                  3.9.0           31_hb3479ef_openblas    conda-forge
libcxx                    19.1.7               ha82da77_0    conda-forge
libexpat                  2.6.4                h286801f_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
liblapack                 3.9.0           31_hc9a63f6_openblas    conda-forge
liblzma                   5.6.4                h39f12f2_0    conda-forge
libopenblas               0.3.29          openmp_hf332438_0    conda-forge
libsqlite                 3.49.1               h3f77e49_1    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
llvm-openmp               19.1.7               hdb05f8b_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_1    conda-forge
ncurses                   6.5                  h5e97a16_3    conda-forge
numpy                     2.2.3           py312h7c1f314_0    conda-forge
openssl                   3.4.1                h81ee809_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_1    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pickleshare               0.7.5           pyhd8ed1ab_1004    conda-forge
pip                       25.0.1             pyh8b19718_0    conda-forge
prompt-toolkit            3.0.50             pyha770c72_0    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pygments                  2.19.1             pyhd8ed1ab_0    conda-forge
python                    3.12.9          hc22306f_0_cpython    conda-forge
python_abi                3.12                    5_cp312    conda-forge
readline                  8.2                  h1d1bf99_2    conda-forge
setuptools                75.8.0             pyhff2d567_0    conda-forge
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
tzdata                    2025a                h78e105d_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forg

Error:

Python 3.12.9 | packaged by conda-forge | (main, Feb 14 2025, 07:56:32) [Clang 18.1.8 ]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.32.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import numpy as np
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/__init__.py:23
     22 try:
---> 23     from . import multiarray
     24 except ImportError as exc:

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/multiarray.py:10
      9 import functools
---> 10 from . import overrides
     11 from . import _multiarray_umath

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/overrides.py:7
      6 from .._utils._inspect import getargspec
----> 7 from numpy._core._multiarray_umath import (
      8     add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
     11 ARRAY_FUNCTIONS = set()

ImportError: dlopen(/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <CAA510D4-816A-34E5-9021-485EF5D56159> /Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libopenblas.0.dylib
  Reason: tried: '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

ImportError                               Traceback (most recent call last)
File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/__init__.py:114
    113 try:
--> 114     from numpy.__config__ import show_config
    115 except ImportError as e:

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/__config__.py:4
      3 from enum import Enum
----> 4 from numpy._core._multiarray_umath import (
      5     __cpu_features__,
      6     __cpu_baseline__,
      7     __cpu_dispatch__,
      8 )
     10 __all__ = ["show_config"]

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/__init__.py:49
     26     msg = """
     27 
     28 IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
   (...)
     47 """ % (sys.version_info[0], sys.version_info[1], sys.executable,
     48         __version__, exc)
---> 49     raise ImportError(msg)
     50 finally:

ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.12 from "/Users/jeffreybaker/miniforge3/envs/spyder-env/bin/python3.12"
  * The NumPy version is: "2.2.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <CAA510D4-816A-34E5-9021-485EF5D56159> /Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libopenblas.0.dylib
  Reason: tried: '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Users/jeffreybaker/miniforge3/envs/spyder-env/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)


The above exception was the direct cause of the following exception:

ImportError                               Traceback (most recent call last)
Cell In[1], line 1
----> 1 import numpy as np

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/__init__.py:119
    115 except ImportError as e:
    116     msg = """Error importing numpy: you should not try to import numpy from
    117     its source directory; please exit the numpy source tree, and relaunch
    118     your python interpreter from there."""
--> 119     raise ImportError(msg) from e
    121 from . import _core
    122 from ._core import (
    123     False_, ScalarType, True_,
    124     abs, absolute, acos, acosh, add, all, allclose,
   (...)
    169     vecmat, void, vstack, where, zeros, zeros_like
    170 )

ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Thank you in advance for your help and patience.

[isuruf]

What's

otool -l /Users/jeffreybaker/miniforge3/envs/test-env/lib/libopenblas.0.dylib

[andyfaff]

I tried to reproduce, but can't. I am on Sequoia 15.3.1, and use miniforge updated to the most recent conda release version, which is 24.11.3. From one of the traces you apparently have 25.1.1. How did you install miniforge?

• I created and activated a test env.
• I conda installed numpy 2.2.3 (from the conda-forge channel) into that test env.
• I can import numpy in a python interpreter in that test env.

[andyfaff]

I note that miniforge version 25.1.1 is a pre-release. I wonder if that could be an issue. What happens if you roll back to miniforge version 24.11.3?

[bakj1979]

Thanks for trying to reproduce.

I re-installed miniforge yesterday night from https://conda-forge.org/download/ and have the same issue with 24.11.3 unfortunately.

I literally wiped my hard drive and reinstalled Sequoia then miniforge, so unsure what the problem could be.

ImportError                               Traceback (most recent call last)
Cell In[5], line 1
----> 1 import numpy; numpy.show_runtime()

File ~/miniforge3/envs/spyder-env/lib/python3.12/site-packages/numpy/__init__.py:119
    115 except ImportError as e:
    116     msg = """Error importing numpy: you should not try to import numpy from
    117     its source directory; please exit the numpy source tree, and relaunch
    118     your python interpreter from there."""
--> 119     raise ImportError(msg) from e
    121 from . import _core
    122 from ._core import (
    123     False_, ScalarType, True_,
    124     abs, absolute, acos, acosh, add, all, allclose,
   (...)
    169     vecmat, void, vstack, where, zeros, zeros_like
    170 )

ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

In [6]: conda --version
conda 24.11.3