I'll try to get clearer on the basilisk situation; I forked your repo and will plunge in soon. It may take a while. In the mean time I hope the BBS python stack can be looked at to see what the issue might be. @Jennifer Wokaty is it possible with the recent R upgrades that tensorflow and tensorflow-probability might need to be installed/updated?
On Wed, Jul 5, 2023 at 3:01 PM Kim Philipp Jablonski <kim.philipp.jablon...@gmail.com> wrote: > > 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 the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline >> <http://www.partners.org/complianceline> . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. -- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
