[Bioc-devel] Python module "tensorflow_probability" not found

[Kim Philipp Jablonski]

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 <stvjc using 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.jablonski using 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]]
> >
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