Closed skearnes closed 1 month ago
The symbolic link here is not being included in the installed package: https://github.com/conda-forge/rdkit-feedstock/blob/5377ec318d340a2ba067b24494d8c48a3ced45e9/recipe/install.sh#L36
test=# create extension rdkit; ERROR: could not access file "$libdir/rdkit": No such file or directory
Manually adding the link fixes the issue:
cd $(pg_config --pkglibdir) ln -s rdkit.so rdkit.dylib
I'm testing alternatives to the symbolic link in install.sh, but I wonder if @jaimergp has ideas about why this isn't working as-is?
# packages in environment at /Users/skearnes/mambaforge/envs/ord: # # Name Version Build Channel annotated-types 0.7.0 pypi_0 pypi anyio 4.4.0 pypi_0 pypi appnope 0.1.4 pypi_0 pypi argon2-cffi 23.1.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arrow 1.3.0 pypi_0 pypi asn1crypto 1.5.1 pypi_0 pypi astroid 3.2.4 pypi_0 pypi asttokens 2.4.1 pypi_0 pypi async-lru 2.0.4 pypi_0 pypi attrs 23.2.0 pypi_0 pypi babel 2.15.0 pypi_0 pypi beautifulsoup4 4.12.3 pypi_0 pypi black 24.4.2 pypi_0 pypi bleach 6.1.0 pypi_0 pypi blinker 1.8.2 pypi_0 pypi bzip2 1.0.8 h99b78c6_7 conda-forge ca-certificates 2024.7.4 hf0a4a13_0 conda-forge cairo 1.18.0 hb4a6bf7_3 conda-forge certifi 2024.7.4 pypi_0 pypi cffi 1.16.0 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi click 8.1.7 pypi_0 pypi comm 0.2.2 pypi_0 pypi coverage 7.6.0 pypi_0 pypi cryptography 43.0.0 pypi_0 pypi debugpy 1.8.2 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi deprecated 1.2.14 pypi_0 pypi dill 0.3.8 pypi_0 pypi dnspython 2.6.1 pypi_0 pypi docopt 0.6.2 pypi_0 pypi email-validator 2.2.0 pypi_0 pypi et-xmlfile 1.1.0 pypi_0 pypi execnet 2.1.1 pypi_0 pypi executing 2.0.1 pypi_0 pypi expat 2.6.2 hebf3989_0 conda-forge fastapi 0.111.1 pypi_0 pypi fastapi-cli 0.0.4 pypi_0 pypi fastjsonschema 2.20.0 pypi_0 pypi flask 3.0.3 pypi_0 pypi font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h82840c6_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fqdn 1.5.1 pypi_0 pypi freetype 2.12.1 hadb7bae_2 conda-forge gunicorn 22.0.0 pypi_0 pypi h11 0.14.0 pypi_0 pypi httpcore 1.0.5 pypi_0 pypi httptools 0.6.1 pypi_0 pypi httpx 0.27.0 pypi_0 pypi icu 75.1 hfee45f7_0 conda-forge idna 3.7 pypi_0 pypi immutabledict 4.2.0 pypi_0 pypi importlab 0.8.1 pypi_0 pypi inflection 0.5.1 pypi_0 pypi iniconfig 2.0.0 pypi_0 pypi ipykernel 6.29.5 pypi_0 pypi ipython 8.26.0 pypi_0 pypi ipywidgets 8.1.3 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi isort 5.13.2 pypi_0 pypi itsdangerous 2.2.0 pypi_0 pypi jedi 0.19.1 pypi_0 pypi jinja2 3.1.4 pypi_0 pypi joblib 1.4.2 pypi_0 pypi json5 0.9.25 pypi_0 pypi jsonpointer 3.0.0 pypi_0 pypi jsonschema 4.23.0 pypi_0 pypi jsonschema-specifications 2023.12.1 pypi_0 pypi jupyter 1.0.0 pypi_0 pypi jupyter-client 8.6.2 pypi_0 pypi jupyter-console 6.6.3 pypi_0 pypi jupyter-core 5.7.2 pypi_0 pypi jupyter-events 0.10.0 pypi_0 pypi jupyter-lsp 2.2.5 pypi_0 pypi jupyter-server 2.14.2 pypi_0 pypi jupyter-server-terminals 0.5.3 pypi_0 pypi jupyterlab 4.2.4 pypi_0 pypi jupyterlab-pygments 0.3.0 pypi_0 pypi jupyterlab-server 2.27.3 pypi_0 pypi jupyterlab-widgets 3.0.11 pypi_0 pypi krb5 1.21.3 h237132a_0 conda-forge libboost 1.84.0 hf763ba5_4 conda-forge libcst 1.4.0 pypi_0 pypi libcxx 18.1.8 h167917d_0 conda-forge libedit 3.1.20191231 hc8eb9b7_2 conda-forge libexpat 2.6.2 hebf3989_0 conda-forge libffi 3.4.2 h3422bc3_5 conda-forge libglib 2.80.3 h59d46d9_1 conda-forge libiconv 1.17 h0d3ecfb_2 conda-forge libintl 0.22.5 h8fbad5d_2 conda-forge libpng 1.6.43 h091b4b1_0 conda-forge libpq 16.3 h7afe498_0 conda-forge librdkit 2024.03.5 h54a62e4_1 conda-forge libsqlite 3.46.0 hfb93653_0 conda-forge libxml2 2.12.7 h01dff8b_4 conda-forge libzlib 1.3.1 hfb2fe0b_1 conda-forge markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib-inline 0.1.7 pypi_0 pypi mccabe 0.7.0 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi mistune 3.0.2 pypi_0 pypi msgspec 0.18.6 pypi_0 pypi mypy-extensions 1.0.0 pypi_0 pypi nbclient 0.10.0 pypi_0 pypi nbconvert 7.16.4 pypi_0 pypi nbformat 5.10.4 pypi_0 pypi ncurses 6.5 hb89a1cb_0 conda-forge nest-asyncio 1.6.0 pypi_0 pypi networkx 3.1 pypi_0 pypi ninja 1.11.1.1 pypi_0 pypi notebook 7.2.1 pypi_0 pypi notebook-shim 0.2.4 pypi_0 pypi numpy 1.26.4 pypi_0 pypi openpyxl 3.1.5 pypi_0 pypi openssl 3.3.1 hfb2fe0b_2 conda-forge ord-interface 0.0.0 pypi_0 pypi ord-schema 0.3.88 pypi_0 pypi overrides 7.7.0 pypi_0 pypi packaging 24.1 pypi_0 pypi pandas 2.2.2 pypi_0 pypi pandocfilters 1.5.1 pypi_0 pypi parso 0.8.4 pypi_0 pypi pathspec 0.12.1 pypi_0 pypi pcre2 10.44 h297a79d_0 conda-forge pexpect 4.9.0 pypi_0 pypi pg8000 1.31.2 pypi_0 pypi pillow 10.4.0 pypi_0 pypi pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.4 hebf3989_0 conda-forge platformdirs 4.2.2 pypi_0 pypi pluggy 1.5.0 pypi_0 pypi postgresql 16.3 hdfa2ec6_0 conda-forge prometheus-client 0.20.0 pypi_0 pypi prompt-toolkit 3.0.47 pypi_0 pypi protobuf 4.22.3 pypi_0 pypi psutil 6.0.0 pypi_0 pypi psycopg 3.2.1 pypi_0 pypi psycopg-binary 3.2.1 pypi_0 pypi psycopg-pool 3.2.2 pypi_0 pypi psycopg2-binary 2.9.9 pypi_0 pypi ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.3 pypi_0 pypi pycnite 2024.7.9 pypi_0 pypi pycparser 2.22 pypi_0 pypi pydantic 2.8.2 pypi_0 pypi pydantic-core 2.20.1 pypi_0 pypi pydot 3.0.1 pypi_0 pypi pygithub 2.3.0 pypi_0 pypi pygments 2.18.0 pypi_0 pypi pyjwt 2.8.0 pypi_0 pypi pylint 3.2.6 pypi_0 pypi pynacl 1.5.0 pypi_0 pypi pyparsing 3.1.2 pypi_0 pypi pytest 8.3.1 pypi_0 pypi pytest-cov 5.0.0 pypi_0 pypi pytest-xdist 3.6.1 pypi_0 pypi python 3.11.9 h932a869_0_cpython conda-forge python-dateutil 2.9.0.post0 pypi_0 pypi python-dotenv 1.0.1 pypi_0 pypi python-json-logger 2.0.7 pypi_0 pypi python-multipart 0.0.9 pypi_0 pypi pytype 2024.4.11 pypi_0 pypi pytz 2024.1 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi pyzmq 26.0.3 pypi_0 pypi qtconsole 5.5.2 pypi_0 pypi qtpy 2.4.1 pypi_0 pypi rdkit 2024.3.3 pypi_0 pypi rdkit-postgresql 2024.03.5 h69bff49_1 conda-forge readline 8.2 h92ec313_1 conda-forge referencing 0.35.1 pypi_0 pypi requests 2.32.3 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi rich 13.7.1 pypi_0 pypi rpds-py 0.19.1 pypi_0 pypi scramp 1.4.5 pypi_0 pypi send2trash 1.8.3 pypi_0 pypi setuptools 71.0.4 pyhd8ed1ab_0 conda-forge shellingham 1.5.4 pypi_0 pypi six 1.16.0 pypi_0 pypi sniffio 1.3.1 pypi_0 pypi soupsieve 2.5 pypi_0 pypi sqlalchemy 2.0.31 pypi_0 pypi stack-data 0.6.3 pypi_0 pypi starlette 0.37.2 pypi_0 pypi tabulate 0.9.0 pypi_0 pypi terminado 0.18.1 pypi_0 pypi testing-common-database 2.0.3 pypi_0 pypi testing-postgresql 1.3.0 pypi_0 pypi tinycss2 1.3.0 pypi_0 pypi tk 8.6.13 h5083fa2_1 conda-forge tokenize-rt 5.2.0 pypi_0 pypi toml 0.10.2 pypi_0 pypi tomlkit 0.13.0 pypi_0 pypi tornado 6.4.1 pypi_0 pypi tqdm 4.66.4 pypi_0 pypi traitlets 5.14.3 pypi_0 pypi treon 0.1.4 pypi_0 pypi typer 0.12.3 pypi_0 pypi types-python-dateutil 2.9.0.20240316 pypi_0 pypi typing-extensions 4.12.2 pypi_0 pypi tzcode 2024a h93a5062_0 conda-forge tzdata 2024.1 pypi_0 pypi uri-template 1.3.0 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi uvicorn 0.30.3 pypi_0 pypi uvloop 0.19.0 pypi_0 pypi watchfiles 0.22.0 pypi_0 pypi wcwidth 0.2.13 pypi_0 pypi webcolors 24.6.0 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.8.0 pypi_0 pypi websockets 12.0 pypi_0 pypi werkzeug 3.0.3 pypi_0 pypi wheel 0.43.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 4.0.11 pypi_0 pypi wrapt 1.16.0 pypi_0 pypi xz 5.2.6 h57fd34a_0 conda-forge zlib 1.3.1 hfb2fe0b_1 conda-forge zstd 1.5.6 hb46c0d2_0 conda-forge
active environment : ord active env location : /Users/skearnes/mambaforge/envs/ord shell level : 2 user config file : /Users/skearnes/.condarc populated config files : /Users/skearnes/mambaforge/.condarc conda version : 24.3.0 conda-build version : not installed python version : 3.10.14.final.0 solver : libmamba (default) virtual packages : __archspec=1=m1 __conda=24.3.0=0 __osx=14.5=0 __unix=0=0 base environment : /Users/skearnes/mambaforge (writable) conda av data dir : /Users/skearnes/mambaforge/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/skearnes/mambaforge/pkgs /Users/skearnes/.conda/pkgs envs directories : /Users/skearnes/mambaforge/envs /Users/skearnes/.conda/envs platform : osx-arm64 user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Darwin/23.5.0 OSX/14.5 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8 UID:GID : 501:20 netrc file : None offline mode : False
Solution to issue cannot be found in the documentation.
Issue
The symbolic link here is not being included in the installed package: https://github.com/conda-forge/rdkit-feedstock/blob/5377ec318d340a2ba067b24494d8c48a3ced45e9/recipe/install.sh#L36
Manually adding the link fixes the issue:
I'm testing alternatives to the symbolic link in install.sh, but I wonder if @jaimergp has ideas about why this isn't working as-is?
Installed packages
Environment info