[Bioc-devel] RcppParallel ABI change. Rebuild Rfast

[Sergio Oller]

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

The bioconductor docker binary repository from

https://bioconductor.org/packages/3.22/container-binaries/bioconductor_docker

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

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>
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> on behalf of Sergio
> Oller <sergioller using gmail.com>
> *Sent:* Wednesday, July 29, 2026 12:48 PM
> *To:* bioc-devel using r-project.org <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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