Thank you all so much for your input and the references! @Kasper: I mostly rely on tensorflow and tensorflow-probability, so I might somehow get rid of the keras dependency but it would require some work.
After being inspired by the lovely orthos package (thanks Charlotte!), I decided to play around further in the basilisk direction and updated my project (https://github.com/cbg-ethz/pareg/tree/feature-basilisk). The hardest part was figuring out a set of package versions which satisfy conda's package manager (@Vincent, I feel you!). But then it just magically worked on my local machine. When testing with GitHub Actions, the windows runner crashes with PackagesNotFoundError: The following packages are not available from current channels: - tensorflow=2.11.1 A look at conda-forge (https://anaconda.org/conda-forge/tensorflow) reveals that for win-64, there's only v1.14.0 available... I guess ignoring the windows build is not an option for my bioc package? For the ubuntu runner, my vignettes were created successfully ("* creating vignettes ... OK"). My tests still fail, but that is expected because I have not wrapped them with basiliskRun. Do I have to do this manually for every function call which may interact with tensorflow (so much boilerplate), or can I somehow implicitly use the created conda env for every function in my package? On Thu, Jul 6, 2023 at 2:08 PM Vincent Carey <st...@channing.harvard.edu> wrote: > That's great news. FWIW I am finding that the advice at > https://rstudio.github.io/reticulate/articles/python_dependencies.html > can work to produce properly resolved python dependencies. Just don't > follow the example literally; the requested > scipy version may not exist. Version 1.11.1 does. Stay tuned. > > On Thu, Jul 6, 2023 at 7:43 AM Charlotte Soneson < > charlottesone...@gmail.com> > wrote: > > > Hi, > > > > in case it's useful: we have a package (orthos) in review ( > > https://github.com/Bioconductor/Contributions/issues/3042) which uses > > basilisk to set up a conda environment with tensorflow and keras. It > builds > > and runs fine both on GitHub Actions (GitHub repo here: > > https://github.com/fmicompbio/orthos) and on the Single Package Builder. > > We have also tested (locally) that it will use GPUs if available, and > that > > the GPU configuration can be controlled from the R session (outside of > the > > package), e.g. by setting the CUDA_VISIBLE_DEVICES environment variable. > > > > Charlotte > > > > > On 5 Jul 2023, at 23:12, Kasper Daniel Hansen < > > kasperdanielhan...@gmail.com> wrote: > > > > > > So I think Kim is interfacing to tensorflow by using the keras package > > from > > > CRAN (partly authored by the Rstudio people). This package leaves it to > > the > > > user to install tensorflow, which is a highly non-trivial installation > > > task. There is some partly helpful instructions for using conda > together > > > with reticulate (see the macOS tab on > > > https://tensorflow.rstudio.com/install/local_gpu.html). This is the > job > > > that basilisk handles for you. In essence, basilisk allows the > developer > > to > > > specify an R-package-specific conda. Tensorflow can be run on a CPUor a > > > GPU. Getting it to run on a user-GPU is extra complicated and I am not > > sure > > > basilisk can handle this. > > > > > > Going forward, we (Bioc) want to decide if we want to support keras on > > our > > > build system. This will require some work, because it is definitely not > > > trivial to get to work (but much more possible if we limit ourselves to > > > running on CPU). If we decide to support keras, we should try to figure > > out > > > how to wrap keras into a basilisk container; perhaps something like > > > creating a keras-basilisk R package, because IF we decide to support > > keras, > > > this is going to be a major headache (to add to the frustration, > > tensorflow > > > often rearranges everything so I future issues keeping it operational). > > > > > > For Kim: I think you should consider if there are any alternatives to > > > keras. Even if we get it to work on our build system, users will have > > major > > > headache getting this to work (I think). If there are no alternatives > to > > > keras, you should perhaps think about doing the keras-basilisk option I > > > outline above (assuming that is feasible; I don't know how keras > > interfaces > > > with tensorflow. You might also have major headaches in your future: I > > have > > > found quite big differences in convergence and optimizers over time in > TF > > > and you're basically saying it should work with every version of > > tensorflow > > >> = 2.2. That's a .... strong promise considering also the difference > > > between GPU and CPU. > > > > > > In the meantime, in case the core build team wants some input, I have > > some > > > experience with tensorflow, although so far my experience is mostly > > > frustration. > > > > > > Best, > > > Kasper > > > > > > > > > On Wed, Jul 5, 2023 at 3:12 PM Vincent Carey < > st...@channing.harvard.edu > > > > > > wrote: > > > > > >> 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> . 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