Installation error

[microbluvrsarah]

Hi, I am trying to install ANCOMBC via BiocManager. I downloaded 'cargo' and 'rustc' which it apparently requires, but I'm still getting an error

`
error: failed to parse lock file at: /tmp/RtmplZZ3DA/R.INSTALL3b60e821d313ec/clarabel/src/rust/Cargo.lock

Caused by:
lock file version 4 requires -Znext-lockfile-bump
make: *** [Makevars:39: /tmp/RtmplZZ3DA/R.INSTALL3b60e821d313ec/clarabel/src/rust/target/release/libclarabel.a] Error 101
ERROR: compilation failed for package ‘clarabel’
`

I'm guessing it's a dependency error, but I've no idea what to do.

[microbluvrsarah]

Managed to overcome this issue, but still getting errors for other dependencies, like gnp, gsl, again the cxcr problem probably because the other issues are not fixed. I feel like I've tried everything, updating everything, force install, via github, one by one downloading these packages (to no success). Idk I don't code so I'm very confused what to do T_T

[FrederickHuangLin]

Hi @microbluvrsarah,

Could you let me know your operating system and the Bioconductor version you’re using?

If you’re on a Linux system, there is a known issue related to package capabilities due to a recent update to the CVXR package, which ANCOMBC depends on.

In the meantime, I’d recommend installing an older version of ANCOMBC from GitHub or Bioconductor as a temporary workaround.

Best,

[microbluvrsarah]

Hiii ya indeed I'm on a linux server

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS

If there are other linux users encountering the problem right now, i had to also download a bunch of other things :

For cargo and clarabel install, I had to do this in terminal

# Install latest Rust (which supports v4 lock files)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

# Restart terminal or run:
source "$HOME/.cargo/env"

# Update to latest
cargo install cargo-update
cargo --version  # Should be 1.77+

Before just running a package install with clarabel.

And also ran these:
sudo apt install libgsl-dev, sudo apt-get install libgmp-dev

And finally did this #329 (comment)

[bcordova22]

You can use R4.5 and the newest version of ANCOM 2.12.0.
The issue as pointed out is CVXR; install the version prior to its major upgrade which is 1.10-15 (https://cran.isid.ac.in/web/packages/CVXR/news/news.html). You can always update it later when necessary.