[Bioc-devel] RcppParallel ABI change. Rebuild Rfast

[Andres Wokaty]

Hi Sergio,

Rfast in the RELEASE_3_22 container is archived, so there won't be a new build. As you suggested, a user could reinstall or use a newer container.

Andres Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Sergio Oller <sergioller using gmail.com>
Sent: Wednesday, September 2, 2026 3:42 AM
To: Andres Wokaty <Andres.Wokaty using sph.cuny.edu>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] RcppParallel ABI change. Rebuild Rfast

Hi Andres,

Thank you for the Rfast rebuild. I could verify it now works.

However, according to

https://github.com/RfastOfficial/Rfast/issues/140#issuecomment-5505356613<https://urldefense.com/v3/__https://github.com/RfastOfficial/Rfast/issues/140*issuecomment-5505356613__;Iw!!LRXxDv2l!Rob5UEizN9MLqJh6qWUl4PFL1uQmuVlqufKk6dHKLI5bHzN0sEpPKvZOZ1lZQC6YsXABn6ICr1BP8DfTExmH-MEhSgc$>

The bioconductor docker binary repository from

https://bioconductor.org/packages/3.22/container-binaries/bioconductor_docker<https://urldefense.com/v3/__https://bioconductor.org/packages/3.22/container-binaries/bioconductor_docker__;!!LRXxDv2l!Rob5UEizN9MLqJh6qWUl4PFL1uQmuVlqufKk6dHKLI5bHzN0sEpPKvZOZ1lZQC6YsXABn6ICr1BP8DfTExmHbeZafis$>

still seems to require a rebuild.

I don't know if that's archived and won't receive the rebuild, although I believe it is worth reporting it just in case.

I understand the container binaries from bioconductor are meant to speed up package installation in containers. Since August 2026,  the Posit Public Package Manager now provides binary Bioconductor packages besides binary CRAN packages, so I guess that would be a valid alternative to container binaries if necessary.

https://packagemanager.posit.co/client/#/repos/bioconductor/setup<https://urldefense.com/v3/__https://packagemanager.posit.co/client/*/repos/bioconductor/setup__;Iw!!LRXxDv2l!Rob5UEizN9MLqJh6qWUl4PFL1uQmuVlqufKk6dHKLI5bHzN0sEpPKvZOZ1lZQC6YsXABn6ICr1BP8DfTExmH0NJ1UZ0$>

In summary, thank you very much for the Rfast rebuild and please consider whether a rebuild of the Rfast package in the container-binaries repository is still possible and worth it.

Have a great day,

Sergi

El dc., 29 de jul. 2026, 20:33, Andres Wokaty <Andres.Wokaty using sph.cuny.edu<mailto:Andres.Wokaty using sph.cuny.edu>> va escriure:
Hi Sergi,

Thanks for reaching out. I've reinstalled Rfast on our two linux machines. and was able to build  AlpsNMR and install PhyloProfile. We should see improvement on tomorrow's build reports.

Andres Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Sergio Oller <sergioller using gmail.com<mailto:sergioller using gmail.com>>
Sent: Wednesday, July 29, 2026 12:48 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: [Bioc-devel] RcppParallel ABI change. Rebuild Rfast

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

Hi,

I'm getting weird missing symbols on the AlpsNMR.

https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.24/bioc-LATEST/AlpsNMR/nebbiolo2-buildsrc.html__;!!LRXxDv2l!SbRpP6FXh8h1igiRB7CFadEHQDGK3nCNMCpKY3G8sfRl-YYKE-Ks5dMfYCOophjlHFtEpKR_8Ni9QBfUnU0ZjSzKBJ5hXQ$

Other packages such as PhyloProfile have the same issue on netbiolo1

https://urldefense.com/v3/__https://bioconductor.org/checkResults/3.23/bioc-LATEST/PhyloProfile/nebbiolo1-install.html__;!!LRXxDv2l!SbRpP6FXh8h1igiRB7CFadEHQDGK3nCNMCpKY3G8sfRl-YYKE-Ks5dMfYCOophjlHFtEpKR_8Ni9QBfUnU0ZjSzdo27_4w$

I didn't find any message from PhyloProfile maintainer, apologies if I
missed it.

According to Kevin Ushey there's an ABI change on RcppParallel 6.0.0 that
requires a rebuild of Rfast.

https://urldefense.com/v3/__https://github.com/RfastOfficial/Rfast/issues/140__;!!LRXxDv2l!SbRpP6FXh8h1igiRB7CFadEHQDGK3nCNMCpKY3G8sfRl-YYKE-Ks5dMfYCOophjlHFtEpKR_8Ni9QBfUnU0ZjSw7UumXhA$

Other (reverse?) dependencies of RcppParallel may require a rebuild as well.

Would you mind triggering a rebuild of the Rfast package on those servers,
so those issues get corrected? (Both -devel and -release channels are
affected in my case)

Thanks,

Sergi

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