Invalid option: --with-python3

[aurimas13]

I am trying to install rdkit on my Macbook Pro through brew, but when I run: brew install rdkit --with-python I get this: Error: Invalid option. I am running the newest version of Big Sur (11.2.3). Can you help me to install rdkit with python 3? As I understand brew removed --with-python, so a question is how to install RDkit with Homebrew?

I will look forward to all the responses.

Sincerely, Aurimas

[UnixJunkie]

try --with-python3 and tell me if it fixes your problem

[aurimas13]

Same issue still. It says invalid option: --with-python3

[UnixJunkie]

Can you show the exact command you are using, full line?

[aurimas13]

Of course.

I am writing this command in terminal:

brew install rdkit --with-python3

[UnixJunkie]

Did you do

brew tap rdkit/rdkit

before? It is needed.

[aurimas13]

Yeah. I've done the command you mentioned but still am getting invalid error when running:

brew install rdkit --with-python3

[UnixJunkie]

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"

[aurimas13]

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?

[YoshitakaMo]

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

[UnixJunkie]

@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__)

[UnixJunkie]

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).

[UnixJunkie]

I am closing this, I am sure the formula here supports --with-python3.

[wenchengxucool]

still have this problem

[nirajkamal]

I have this problem too, after latest Mac upgrade

[nirajkamal]

brew install vim --with-python3

this command shows this: Error: invalid option: --with-python3

[nirajkamal]

@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: https://github.com/Homebrew/homebrew-core/issues/31510