rdkit-sys question

[jhylin]

Hi,

I’m a relatively new user of Rust (more familiar with Python & R) and hoping to integrate Rust and RDKit (trying to start a cheminformatics project in Rust), so I was quite excited to come across this crate, rdkit-sys, online. I was running it on VS code on Mac OS, by using the latest version 0.2.16 of rdkit-sys in the cargo.toml. However, when I ran it via cargo check or cargo test, it showed a set of errors like this after compilation (in total it appeared twice):

warning: /usr/local/include/rdkit/RDGeneral/Dict.h:261:26: error: no template named 'is_same_v' in namespace 'std'; did you mean 'is_same'?
warning: static_assert(! std::is_same_v<T, std::string_view>,
warning: ~~~~~^~~~~~~~~
warning: is_same

warning: /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/type_traits:547:61: note: 'is_same' declared here
warning: template <class _Tp, class _Up> struct _LIBCPP_TEMPLATE_VIS is_same : public false_type {};
warning:

Prior to this, I’ve already installed rdkit and relevant dependencies via Homebrew. It appeared there might be conflicts between one of the RDKit files and one of the llvm files (this was as far as I could tell if I went back to these files). So either I’m missing something obvious here (being quite new in the coding world) or I wasn’t doing something correctly?

Hoping someone might be able to enlighten me on this one... (might be due to a silly thing I've missed).

Many thanks,
J

[xrl]

Interesting, I wonder if rdkit-rs needs to updates how it builds the load path for rdkit. Can you post your rdkit version? brew info rdkit should have it.

[jhylin]

Hi,

This was what I've got for my RDKit version (I actually uninstalled RDKit and re-installed it after having this problem, but it still persisted after the re-installation):

==> rdkit: stable 2022.09.1 (bottled), HEAD
Open-source chemoinformatics library
https://rdkit.org/
/usr/local/Cellar/rdkit/2022.09.1 (1,856 files, 177.2MB) *
Poured from bottle on 2022-11-28 at 13:37:49
From: https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/rdkit.rb
License: BSD-3-Clause
==> Dependencies
Build: cmake ✔, swig ✔
Required: boost ✔, boost-python3 ✔, eigen ✔, freetype ✔, numpy ✔, postgresql@14 ✔, py3cairo ✔, python@3.10 ✔
==> Options
--HEAD
Install HEAD version
==> Caveats
You may need to add RDBASE to your environment variables.
For Bash, put something like this in your $HOME/.bashrc:
export RDBASE=/usr/local/opt/rdkit/share/RDKit
==> Analytics
install: 404 (30 days), 1,324 (90 days), 4,381 (365 days)
install-on-request: 218 (30 days), 715 (90 days), 2,844 (365 days)
build-error: 0 (30 days)

Thanks,
J

[jhylin]

I'll close this issue for now, as I've found other tools to work with. Would love to know if rdkit-rs actually needs to update how it builds the load path to rdkit. Thanks for responding in the first place anyway.