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

[Francesc Catala Moll]

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://url.de.m.mimecastprotect.com/s/bZduCpZNRmiZlMYCPfBTGZuUj
>>
>> 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
>>>
>>>         [[alternative HTML version deleted]]
>>>
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>>>
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