[Bioc-devel] Rust compilation environment in Bioconductor

[Andres Wokaty]

cargo is installed on the Linux devel builder, but in a different location

biocbuild using nebbiolo1:~$ which cargo
/usr/bin/cargo
biocbuild using nebbiolo1:~$ cargo --version
cargo 1.75.0

We generally prefer to apt install dependencies on the Linux builders, which might be why the path is different. It is not currently installed on any of the macs or Windows machines, but I can install it on them next week.


Andres Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Sun Wenjie <sunwjie using gmail.com>
Sent: Monday, March 3, 2025 6:40 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Rust compilation environment in Bioconductor

* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *

Hello,

I recently tried to translate Rcpp to Rust using extendr for my package. However, I encountered a compilation error in Bioc.

I'm unsure whether the issue is with my package configuration or if Bioconductor lacks the necessary Rust environment. Could someone provide some suggestions?

Here is the Bioc checkResults:
https://urldefense.com/v3/__https://www.bioconductor.org/checkResults/3.21/bioc-LATEST/CellBarcode/__;!!LRXxDv2l!VfHUcNvgTi02vTeBmtsZvdw94LBgyKc6BO-A3r-2JNxEbGF_ZeoWSiJQw5yazbNz5A-4MmxNeS6UQDvf0bRoXWNdOA$

The main problem is the absence of `cargo`, as indicated by the error message:
`/bin/sh: line 6: cargo: command not found`

By the way, the package passed the check on GitHub Actions: https://urldefense.com/v3/__https://github.com/wenjie1991/CellBarcode/actions/runs/13597209989__;!!LRXxDv2l!VfHUcNvgTi02vTeBmtsZvdw94LBgyKc6BO-A3r-2JNxEbGF_ZeoWSiJQw5yazbNz5A-4MmxNeS6UQDvf0bQlsR4RsQ$

Thank you,
Wenjie

------------------------------------------
Wenjie SUN
Postdoctoral researcher
UMR168, Curie Institute
E-mail: wenjie.sun using curie.fr
Address: batiment Curie, RDC.13A
11 rue Pierre et Marie Curie, 75005 Paris
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