Thanks a lot for your response! The Config/reticulate approach in DESCRIPTION looks very neat. I hope we can use it at some point.
Could the issue you are facing with the conda install be, that the package is called "tensorflow-probability" instead of "tensorflow_probability" ( https://anaconda.org/conda-forge/tensorflow-probability)? I have followed the basilisk advice and incorporated it into my package here: https://github.com/cbg-ethz/pareg/tree/feature-basilisk. The basilisk docs say "Any R functions that use Python code should do so via basiliskRun()". This does not seem possible in my case as I am using tensorflow(probability) wrappers instead of calling them directly. Building the vignettes with Github Actions fails because tensorflow could not be found: https://github.com/cbg-ethz/pareg/actions/runs/5466980003/jobs/9952690137#step:15:39 (I might have to activate basilisk somehow, but using basiliskStart seems to only make sense with basiliskRun). I could also not find any advice on this elsewhere. Do you have a suggestion how to best handle this (or should it *just* work)? On Tue, Jul 4, 2023 at 1:04 PM Vincent Carey <st...@channing.harvard.edu> wrote: > 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 th...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
