Hi everyone, I am dealing with a similar situation involving an R package that sources Julia code. One approach we are considering is to provide parallel implementations in both R and Julia, with the package defaulting to the Julia backend when available and automatically falling back to a pure R implementation otherwise. This would allow the package to remain usable without a Julia installation, while still benefiting from Julia’s performance when present.
Would such a design be considered reasonable, and potentially acceptable, for a Bioconductor submission? Kind regards, Ali On Tue, 3 Feb 2026 at 10:26, Verena Korber via Bioc-devel < [email protected]> wrote: > Hi both, > > Many thanks for your detailed responses. The reason we want to build the > package on Julia is that we use approximate Bayesian Computation, which > runs significantly faster in Julia than in R. You’re probably right that > compiling on C++ would be more straightforward and I see the points you > make. My senses was it would be nice to have an R interface as this is more > accessible to many users but reading your responses, I think that’s > probably not the way to take things forward. > > Many thanks again for your help and all the best, > > Verena > > > On 30 Jan 2026, at 20:06, Nanda, Pariksheet <[email protected]> wrote: > > > > Hi Verena, > > > > Polyglot code can be tricky as Hervé points out. Another option, if > you're open to using Rcpp in your Bioconductor package, is the mlpack C++ > header-only library that interfaces with Julia, R, Python, and Go ( > mlpack.org) and there is a spack package that may simplify the > installation for you (packages.spack.io/package.html?name=mlpack) if > you're not keen on containers and/or prefer native architecture compilation. > > > > That way, you're specifying an external dependency on mlpack only for > which you can also create an R package (CRAN has plenty of C++ header-only > packages you can refer to) and to Hervé's point you could limit certain > unit tests that are julia-specific to CI systems that provide that > functionality (perhaps your own). > > > > I don't use mlpack and don't know how well it would suit your purpose; > you don't describe what Julia packages or functionality you're using the > Julia code for. mlpack is the only relevant result that showed up from > searching for polyglot r packages in the spack repository with julia [1]. > > > > As Hervé mentions, you would have to think carefully about your user > setup experience and how maintainable it would be to have robust packaging > with Julia code compared to rewriting the Julia code into existing R > packages or setup that requires fewer additional steps and moving parts. I > don't meant to discourage you from what you're doing: polyglot code is more > common and in large scientific codes but can need a bit of work to maintain > within language-specific package managers or require a language-agnostic > package manager. > > > > Pariksheet > > > > [1] Namely: > > git clone https://github.com/spack/spack.git spack > > cd spack > > source share/spack/setup-env.sh > > spack repo update > > spack cd -P > > grep -lw r packages/*/*.py | xargs grep -F julia > > less packages/mlpack/package.py > > > > ________________________________________ > > From: Bioc-devel <[email protected]> on behalf of Hervé > Pagès <[email protected]> > > Sent: Friday, January 30, 2026 1:26 PM > > To: Verena Korber; [email protected] > > Subject: Re: [Bioc-devel] Bioconductor package based on Julia? > > > > Hi Verena, > > > > I personally don't have any experience with using Julia within an R > > package, and I don't think we have any packages in Bioconductor that do > > this at the moment. As you mentioned, the implication is that users will > > need a Julia installation for the package to run. Ask yourself how many > > users are going to be comfortable doing this. I don't know how > > mainstream Julia has become at this point, and how easy it is to > > install. Is it available on the 4 major platforms that we officially > > support, i.e. on Linux, Windows, Intel Mac, and Mac Silicon? > > > > It also means that we will need to install Julia on our build machines. > > And also that, in the near future, the builds on r-universe will be able > > to accommodate this requirement (I'm mentioning this in the context of > > an ongoing effort by the core team to move the Bioconductor daily builds > > to the r-universe build facilities). > > > > At the very least, you'll need to: > > > > 1. List Julia in the SystemRequirements field of the package. > > > > 2. Provide an INSTALL file that explains how to install Julia on the 4 > > major platforms that we support. See > > https://contributions.bioconductor.org/sysdep.html?q=install#sysdep > > > > They have JuliaCall and JuliaConnectoR on CRAN for interfacing R with > > Julia code, which I'm not familiar with either, but it seems to me that > > you'd want to leverage that. > > > > Sorry for the very generic answer. Hopefully someone on this mailing > > list has some experience with Julia in R and can give more useful > > recommendations. > > > > Best, > > > > H. > > > > > > On 15/01/2026 08:47, Verena Korber via Bioc-devel wrote: > >> Hello, > >> > >> We are currently developing an R package that sources Julia code. Is it > possible to submit sth. like this to Bioconductor and if so, what would the > requirements be? I guess one challenge is that users would need a Julia > installation for the package to run. If anyone has any experience in that > direction, it would be super helpful. > >> > >> Many thanks and kind regards, > >> > >> Verena > >> _______________________________________________ > >> [email protected] mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > > Hervé Pagès > > > > Bioconductor Core Team > > [email protected] > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
