conda skeleton install R package from github

[nick-youngblut]

If possible, I'd like to install an R package into my conda environment, but the R package is only available on GitHub. Is there any way that I can use conda skeleton to create a conda package for this R package, or am I stuck using devtools::install_github within R?

[mingwandroid]

You can just pass the github url to conda skeleton cran. It requires a specific layout (DESCRIPTION file in the root AFAIR). PRs to search for this file in subfolders would be welcomed.

[kalefranz]

PRs to search for this file in subfolders would be welcomed.

In conda-build :)

[nick-youngblut]

Thanks for the quick reply! I'm unclear about what you mean by

It requires a specific layout (DESCRIPTION file in the root AFAIR)

As a test, I tried the following and ran into an error:

$ conda skeleton cran https://github.com/reptalex/phylofactor
Tip: install CacheControl and lockfile (conda packages) to cache the CRAN metadata
Fetching metadata from https://cran.r-project.org/
Parsing input package https://github.com/reptalex/phylofactor:
.. name: phylofactor location: https://github.com/reptalex/phylofactor new_location: /ebio/abt3_projects/software/dev/conda_packages/r-phylofactor
Making/refreshing recipe for phylofactor
Cloning into bare repository '/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/git_cache/github.com/reptalex/phylofactor'...
remote: Counting objects: 2439, done.
remote: Compressing objects: 100% (21/21), done.
remote: Total 2439 (delta 5), reused 12 (delta 3), pack-reused 2415
Receiving objects: 100% (2439/2439), 15.74 MiB | 7.97 MiB/s, done.
Resolving deltas: 100% (1655/1655), done.
Checking connectivity... done.
Cloning into '/ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1515315639680/work'...
done.
checkout: 'HEAD'
Your branch is up-to-date with 'origin/master'.
==> git log -n1 <==

fatal: No names found, cannot describe anything.
commit be62474fe5d2b6100d709f3636e96912757839e2
Author: Alex Washburne <bigalculus@gmail.com>
Date:   Sat Jan 6 09:05:53 2018 -0700

    ...

==> git describe --tags --dirty <==

commit be62474fe5d2b6100d709f3636e96912757839e2
Author: Alex Washburne <bigalculus@gmail.com>
Date:   Sat Jan 6 09:05:53 2018 -0700

    ...

==> git status <==

On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean


Leaving build/test directories:
  Work:	 /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1515315639680/work
  Test:	 /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1515315639680/test_tmp
Leaving build/test environments:
  Test:	source activate  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1515315639680/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac
  Build:	source activate  /ebio/abt3_projects/software/dev/miniconda3_dev/conda-bld/skeleton_1515315639680/_build_env


Error: no tags found

The repo has a DESCRIPTION file, which looks like it's correctly formatted. I don't really understand the no tags found error.

[mingwandroid]

It tries to find the most recent tag and errors out if there are none. You should ask the project if they can make a release and tag it (or else make a PR to conda-build to add an argument for which git reference to use, where no value means latest tag).

BTW, please open issues against conda-build in the conda-build repository. All conda skeleton are actually implemented there (confusing, I know).

[nick-youngblut]

Thanks for the clarification! This should probably be a different thread/issue, but when trying to use conda skeleton cran on many packages (eg., phylosignal), I get dependency errors during the conda-build step. For example:

conda_build.exceptions.DependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {'r-rnexml', "r-rncl[version='>=0.6.0']"}

When I try to then run conda skeleton cran on the dependency R packages (they aren't available on any anaconda channel), I get new errors with their dependencies. Is there any way to automate the process of creating a conda package with conda skeleton cran and also creating packages for all of the dependencies missing in conda channels, or will I need to build each R package separately, starting with the lowest dependencies and working up from there?

Sorry for all of the questions, but I can't find much documentation on using conda skeleton cran. I'm probably just not looking hard enough.

[mingwandroid]

I'm probably just not looking hard enough

Indeed.

conda skeleton cran --help should be err, helpful?

[nick-youngblut]

Yep, you're absolutely right. When I last looked at conda skeleton cran --help, I saw the --no-recursive, but I missed that there as also a --recursive. That's what I get for reading the help too quickly. Sorry to waste your time

[krinsman]

In reference to old comment from above: #6674 (comment)

For anyone else coming here via Google search, a quick workaround to this is forking the repository on GitHub you want to make a conda package from, and then adding a tag to your forked repository, e.g. in the terminal

git clone https://github.com/your_username/forked_repo  destination/forked_repo
cd destination/forked_repo
git tag v0.0.0
git push --tags

Then using e.g. conda skeleton cran https://github.com/your_username/forked_repo on your forked repo will do the trick. This is helpful for version control, e.g. to ensure you make a package from the same commit in the future, or e.g. if the original repo is otherwise destroyed or lost.

[statneutrino]

Hi - I successfully managed to use this method to installr package cmdstanr on Windows conda using the following commands:

conda skeleton cran https://github.com/stan-dev/cmdstanr
conda-build --R 4.1.1 cmdstanr

but now on a different machine on Linux I am getting this error:

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

fatal: unable to access 'https://github.com/stan-dev/cmdstanr/': Could not resolve host: github.com Failed to update local git cache. Deleting local cached repo: /home/statneutrino/anaconda3/conda-bld/git_cache/github.com/stan-dev/cmdstanr Warning: failed to download source. If building, will try again after downloading recipe dependencies.
Error was:
Command '['/home/statneutrino/anaconda3/conda-bld/r-cmdstanr_1633704969477/_build_env/bin/git', 'fetch']' returned non-zero exit status 128. Failed to download or patch source. Please see build log for info.

Can anyone help? I've spent many hours and I feel like I'm almost there...