Comments (16)
Now the homebrew-core (default) repository has the rdkit formula (Release 2020.09.4) and it binds to python3 by default.
brew untap rdkit/rdkit # if required
brew install rdkit
It also has rdkit-postgresql.
See also https://github.com/Homebrew/homebrew-core/blob/master/Formula/rdkit.rb
from homebrew-rdkit.
I am closing this, I am sure the formula here supports --with-python3.
from homebrew-rdkit.
try --with-python3 and tell me if it fixes your problem
from homebrew-rdkit.
Same issue still. It says invalid option: --with-python3
from homebrew-rdkit.
Can you show the exact command you are using, full line?
from homebrew-rdkit.
Of course.
I am writing this command in terminal:
brew install rdkit --with-python3
from homebrew-rdkit.
Did you do
brew tap rdkit/rdkit
before?
It is needed.
from homebrew-rdkit.
Yeah. I've done the command you mentioned but still am getting invalid error when running:
brew install rdkit --with-python3
from homebrew-rdkit.
As a workaround, try the conda install method of rdkit.
For the future, can you create a gist showing the full log of your install attempt?
Out of despair, you should try what is mentioned in this paragraph of the README.md file
of this homebrew recipe:
"Forcing brew to install rdkit and all its dependencies from scratch"
from homebrew-rdkit.
Out of despair I tried to reinstall rdkit from scratch:
brew list --formula > my_brew_packages.txt
brew uninstall --force $(cat my_brew_packages.txt)
brew install rdkit --with-python3
and then again did this:
brew tap rdkit/rdkit
brew install rdkit --with-python3
but in both cases I am still getting:
Error: invalid option: --with-python3
As for conda when I tried the installation with it I don't how to check whether it worked. What should I run to enter rdkit?
Also when I try to install RDKitPostgreSQL I run this:
conda install -c rdkit rdkit-postgresql
it installs everything and then is followed by
/Users/Aurimas/opt/anaconda3/envs/my-rdkit-env/bin/initdb -D /folder/where/data/should/be/stored
which gives:
creating directory /folder/where/data/should/be/stored ... initdb: error: could not create directory "/folder": Read-only file system
How could this be solved?
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@aurimas13
Here is a test script; roundtrip_test.py in this repository:
#!/usr/local/bin/python3.9
# we have to use the python interpreter installed by brew...
# quick check that rdkit is installed and working
# upon success, the installed rdkit version is printed out
# upon failure, an assert will fail or some other error will
# be printed out
import rdkit
from rdkit import Chem
in_smi = 'c1ccncc1'
mol = Chem.MolFromSmiles(in_smi)
out_smi = Chem.MolToSmiles(mol)
assert(in_smi == out_smi)
print(rdkit.__version__)
from homebrew-rdkit.
The fact that there is a new formula with the same name in the master repository of brew might have broke the current formula
(it is silently ignored/overwritten).
from homebrew-rdkit.
still have this problem
from homebrew-rdkit.
I have this problem too, after latest Mac upgrade
from homebrew-rdkit.
brew install vim --with-python3
this command shows this:
Error: invalid option: --with-python3
from homebrew-rdkit.
@UnixJunkie , no it doesn't! it did before, but the latest version doesn't! Please do your research before closing issues.
Options have been removed from Homebrew core formulas and only exist in taps now. See this GitHub issue:
Homebrew/homebrew-core#31510
from homebrew-rdkit.
Related Issues (20)
- update to latest release HOT 2
- Add build with Cairo flag HOT 1
- Installs RDKit/Code into the wrong directory HOT 3
- Failing make at "[ 14%] Built target rdBase" HOT 2
- RDKit installation problem on macOS Big Sur HOT 7
- Installation Not Working HOT 1
- rdpath in dylibs is not set (10.15.7 intel) HOT 11
- rdkit with pyenv HOT 2
- Invalid option --with-python3 HOT 4
- Installation Error on Mac 10.15.2 HOT 4
- Update README to reflect python3 only
- Failure to install on macOS Mojave HOT 12
- Problem with linker while compiling HOT 5
- Could NOT find Boost (missing: python) (found suitable version "1.72.0", minimum required is "1.56.0") HOT 5
- Failed to install on MacOS Mojave 10.14.6 HOT 6
- Build error in Ubuntu 16.04.6 LTS HOT 9
- Add rdkit.egg-info directory HOT 7
- rdkit installation problem in mac os catelina HOT 2
- RDKIt PostgreSQL cartrdige via brew HOT 8
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