Sorry to hear about this. Our informal outlook on python interoperation in Bioconductor packages is that the basilisk discipline should be used. This allows you to pin specific versions of all python dependencies and use python for your R functions from an insulated conda environment.
There is also information about specifying python dependencies in the DESCRIPTION file at https://rstudio.github.io/reticulate/articles/python_dependencies.html I do not know if our build system or R CMD install take effective advantage of that approach at this time. I was surprised to see that my attempt to use reticulate::py_install() to install tensorflow_probabiliity on my laptop failed: '/home/stvjc/.local/share/r-miniconda/bin/conda' 'install' '--yes' '--prefix' '/home/stvjc/.local/share/r-miniconda/envs/r-reticulate' '-c' 'conda-forge' 'tensorflow_probability' Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - tensorflow_probability Current channels: - https://conda.anaconda.org/conda-forge/linux-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. Error: one or more Python packages failed to install [error code 1] Enter a frame number, or 0 to exit 1: py_install("tensorflow_probability") So the "current channels" used by reticulate in my pretty stock installation of R/reticulate seem flawed for this purpose. I had hoped to write a bit of code that would check for the desired module and install it if missing, that you could include in your package. get_pippath = function() { pypath = reticulate::conda_list() |> (\(x)x[x$name=="r-reticulate",])() gsub("python$", "pip", pypath$python) } check_tfp = function() { pippath = get_pippath() peek = system(paste0(pippath, " list | grep tensor"), intern=TRUE) peek = gsub(" +", " ", peek) tfdf = do.call(rbind, lapply(strsplit(peek, " "), function(x) data.frame(pkg=x[1], version=x[2]))) "tensorflow_probability" %in% tfdf$pkg } install_tfp = function() { pippath = get_pippath() chk = system(paste(pippath, "install tensorflow_probability"), intern=TRUE) chk2 = check_tfp() list(sysout=chk, tfp_installed=chk2) } The first two functions seem to do what I want, the latter does not. Suggestion -- read the basilisk vignettes, use it if at all possible. Certainly we can take care of this in our build system when the holiday ends, but it would be great to have the software arrange the solution when necessary, and I don't see a way to accomplish this at the moment. On Tue, Jul 4, 2023 at 5:32 AM Kim Philipp Jablonski <kim.philipp.jablon...@gmail.com> wrote: > > Hello, > > The latest builds of my package 'pareg' started failing on BioC 3.17 for > Linux and macOS but not Windows: > https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/pareg/nebbiolo1-buildsrc.html > . > In both cases, the error messages is "Python module tensorflow_probability > was not found". This wasn't an issue in earlier releases. > > Do you know what the reason for this is and how I can fix it? > Thanks a lot for your help! > > Best regards, > Kim > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- The information in this e-mail is intended only for the ...{{dropped:16}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
