rdpath in dylibs is not set (10.15.7 intel)

[wgscott]

rpath unset in most of the libraries. eg:

otool -L libRDKitSimDivPickers.2020.09.1.dylib | grep rpath
@rpath/libRDKithc.1.dylib (compatibility version 1.0.0, current version 2020.9.1)
@rpath/libRDKitRDGeneral.1.dylib (compatibility version 1.0.0, current version 2020.9.1)

[UnixJunkie]

And so, how should we fix this?

[UnixJunkie]

Also, does this break something?
I just use rdkit from Python and it looks like it is working even if I use this brew installer.

[UnixJunkie]

A pull request to fix/improve this would be welcome.

[YoshitakaMo]

This issue will be solved by adding -DCMAKE_INSTALL_RPATH=#{opt_lib}. See also Homebrew/homebrew-core#71694 .

And I recommend using homebrew-core's rdkit formula instead.

brew untap rdkit/rdkit # if required
brew install rdkit

[UnixJunkie]

@YoshitakaMo if you created a new brew formula for rdkit, and this is to be the standard one, maybe it should be announced on the rdkit-mailing list...
I was not aware of it, despite I try to maintain this recipe, which many people have contributed to over the years.

[YoshitakaMo]

Since RDKit is now also used as a component of other programs such as Coot, I created a new RDKit formula as a byproduct of it.
Also, because the RDKit formula of this repository has not been updated recently and its syntax (e.g. install options such as --with-python3) became outdated, I had to create a new one to pass the homebrew-core's CI.
Although I have tried it with some test scripts, I cannot guarantee its full functionality since I am not a hard-core user of RDKit.

I would like to thank the long-time contributors of this formula. I'll consider announcing it on the mailing list.

[UnixJunkie]

Did you create your formula starting from this one?
If not, I will have to go look the differences, to check that what is here was also included in the new formula.
For example, the formula here even works on Linux homebrew !

The fact that in your new formula, several things are no more optional makes it quite slow to install (not everybody
requires PGSQL, the python wrappers, etc.).

Regards,
Francois.

[YoshitakaMo]

Did you create your formula starting from this one?

Yes, I analyzed the rdkit formula here to create the new one. The basic functionalities are thus almost compatible, but I removed --with-java support and add a new option -DRDK_BUILD_YAEHMOP_SUPPORT=ON, which is used in the conda-rdkit.

For example, the formula here even works on Linux homebrew !

Thank you for this comment. Today I modified the new formula again to enable Linux OS to build rdkit from source. I tested it on my CentOS 7.8 and the installation was succeeded.

The fact that in your new formula, several things are no more optional makes it quite slow to install

I don't think it is such a big problem because homebrew-core provides a "bottle" of pre-compiled rdkit for each OS. This saves a lot of installation time, which is an advantage of using homebrew-core.

A bottle for Linux OS is not ready at this time for some reason, but I think homebrew-core/linuxbrew-core will generate it later.

[UnixJunkie]

You removed the java support because it doesn't compile on a Mac, right?
We have an issue here tracking that, though no solution:
#38

[UnixJunkie]

If you announce your recipe on the mailing-list, many people use the new formula and are happy with it, we might stop maintaining this repository and just pointing to the new one.

The fact that we don't need a tap anymore makes the install simpler.
Also, the new formula uses more modern syntax and looks simpler, embeds a test and enjoys the CI
tests of homebrew-core plus "bottles" !

[YoshitakaMo]

You removed the java support because it doesn't compile on a Mac, right?

Yes, I removed it because I don't have a good idea to include java support. conda-rdkit neither.

If you announce your recipe on the mailing-list, many people use the new formula and are happy with it, we might stop maintaining this repository and just pointing to the new one.

Thanks @UnixJunkie and the contributors here. I will announce on the mailing-list in a few days.