[Bioc-devel] [EXT] Re: Installation Error on nebbiolo2 Due to CVXR Dependency

Tue Apr 21 18:47:09 CEST 2026

Hi everyone,

Sorry for the delayed response. The release is always pretty hectic.

Since we're moving toward an R Universe build where the rust will be available in the container, I updated to a newer rust on nebbiolo1 yesterday, so ANCOMBC is now passing.

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 Francesc Catala Moll via Bioc-devel <bioc-devel using r-project.org>
Sent: Tuesday, April 21, 2026 4:03 AM
To: Huang Lin (Frederick) <huanglinfrederick using gmail.com>; Vincent Carey <stvjc using channing.harvard.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] [EXT] Re: Installation Error on nebbiolo2 Due to CVXR Dependency

* External Sender - Proceed Cautiously with Links and Attachments. *

Dear Huang,

I maintain a package that depends on ANCOMBC and saw the recent Bioc-devel thread regarding the CVXR build failure on nebbiolo1.

To help resolve this quickly, I have just submitted a Pull Request to your GitHub repository. The PR completely removes the CVXR dependency by replacing its single use-case in the trend test with the quadprog package.

quadprog solves the exact same constrained optimization problem but is a lightweight CRAN standard that does not require Rust, meaning it will compile flawlessly on all Bioconductor servers. I have tested it locally to ensure the results perfectly match your original implementation.

I hope you find this PR helpful to get ANCOMBC building smoothly again!

Best regards,

Francesc

De: Bioc-devel <bioc-devel-bounces using r-project.org> en nombre de Huang Lin (Frederick) <huanglinfrederick using gmail.com>
Fecha: lunes, 13 de abril de 2026 a las 18:00
Para: Vincent Carey <stvjc using channing.harvard.edu>
CC: bioc-devel using r-project.org <bioc-devel using r-project.org>
Asunto: [EXT] Re: [Bioc-devel] Installation Error on nebbiolo2 Due to CVXR Dependency

Dear Vincent and BioC Team,

I’m writing to follow up on my previous inquiry, as I am still receiving
the error on nebbiolo1.

Do you anticipate adding rustc support on nebbiolo1 in the future? Also, is
there anything I can do on my end to help resolve this issue?

Thank you so much for your time and assistance,

On Tue, Mar 31, 2026 at 2:50 PM Huang Lin (Frederick) <
huanglinfrederick using gmail.com> wrote:

> Hi Vincent,
>
> Thanks so much for the explanation; that was very helpful.
>
> Since this appears to be more of a system issue, do you anticipate adding
> rustc support on nebbiolo1 in the future? Alternatively, would moving the
> CVXR dependency from Imports to Suggests help in this case?
>
> Best,
>
>
> On Mon, Mar 23, 2026 at 6:47 PM Vincent Carey <stvjc using channing.harvard.edu>
> wrote:
>
>> I suspect that the problem is that clarabel can't compile on nebbiolo1,
>> because rustc is
>> a System Requirement, and we haven't adopted rustc support at this time.
>> CVXR is not
>> buildable in the absence of clarabel, and thus ANCOMBC won't build there
>> either.  The mac binary
>> for CVXR, on the other hand, is available from r-universe, and so there
>> is a successful build for the
>> mac platform.
>>
>> You can learn about the health of your package on linux at
>> https://urldefense.com/v3/__https://url.de.m.mimecastprotect.com/s/bZduCpZNRmiZlMYCPfBTGZuUj__;!!LRXxDv2l!SBAKEdF9h4kmjHXHR1poCSwGgxx66uZGHREXWbtHNxO-QJzr7KBYOf3YuLJYfHVJ-r3WKcVxI3OBXwYYcoKwu7YtpwFzjmAM5A$
>>
>> On Mon, Mar 23, 2026 at 6:11 PM Huang Lin (Frederick) <
>> huanglinfrederick using gmail.com> wrote:
>>
>>> Dear BioC Team,
>>>
>>> I am the maintainer of the ANCOMBC package and have recently received
>>> notifications indicating installation errors on nebbiolo2.
>>>
>>> From the error messages, it appears that the issue is related to the
>>> unavailability of the dependency package ‘CVXR’. I have not observed
>>> similar issues on other platforms, and the ANCOMBC package builds and
>>> installs successfully on my local MacBook.
>>>
>>> Could you advise on how to address this issue?
>>>
>>> Thank you,
>>>
>>> Huang
>>>
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>>>
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>>>
>>
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