[Bioc-devel] Rust compilation environment in Bioconductor

[Sun Wenjie]

Thank you Andres.

Look forward to have the cargo in macs and windows machines next week.

And it is very helpful to know the cargo version in Linux devel builder.
Since the cargo is available, I believe it can be easily fixed through the package configuration.

Best,
Wenjie

> On Mar 4, 2025, at 02:46, Andres Wokaty <Andres.Wokaty using sph.cuny.edu> wrote:
> 
> 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 TeamFrom: 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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