Adding pio r package as r-pio

[brandon-hastings]

Checklist

• Title of this PR is meaningful: e.g. "Adding my_nifty_package", not "updated meta.yaml".
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[conda-forge-admin]

Hi! This is the friendly automated conda-forge-linting service.

I failed to even lint the recipe, probably because of a conda-smithy bug 😢. This likely indicates a problem in your meta.yaml, though. To get a traceback to help figure out what's going on, install conda-smithy and run conda smithy recipe-lint --conda-forge . from the recipe directory. You can also examine the workflow logs for more detail.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/14088621076. Examine the logs at this URL for more detail.}

[github-actions]

Hi! This is the staged-recipes linter and I found some lint.

File-specific lints and/or hints:

• recipes/r-pio/meta.yaml:
  • lints:
    • The following maintainers have not yet confirmed that they are willing to be listed here: BrandonHastings. Please ask them to comment on this PR if they are.

[conda-forge-admin]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/r-pio/meta.yaml) and found it was in an excellent condition.

[github-actions]

Hi! This is the staged-recipes linter and your PR looks excellent! 🚀

[conda-forge-admin]

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/r-pio/meta.yaml) and found some lint.

Here's what I've got...

For recipes/r-pio/meta.yaml:

• ❌ Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [45, 46]

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/14176086676. Examine the logs at this URL for more detail.}

[conda-forge-admin]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/r-pio/meta.yaml) and found it was in an excellent condition.

[mfansler]

Generally, we prefer to work downstream of CRAN. Is there a reason why this package cannot first be deposited there?

[brandon-hastings]

Hi, the reason that the pio package is not on CRAN is that there are similar packages now hosted on CRAN that do the same thing since it is input output highlighting. However, we are in the process of submitting a nextflow pipeline to the nf-core repository that is made up of many previous packages from our lab that are dependent on pio, as at one point our pio package was the only one that gave us the output format we prefer. The nf-core maintainers requested that we repackage some of our custom modules in our submitted pipeline to be standard nf-core modules, which require that they are available in conda. In order to create the conda environment for these modules we first need pio to be available on conda-forge, but did not necessarily plan to submit pio to CRAN since nowadays there are similar packages available. Pio is stable, if it helps, with no need for updates in the past 5 years even with all of our other packages being dependent on it.

[mfansler]

I'd recommend submitting this to Bioconda instead. You can also ping me there for review/merge.

CC: @conda-forge/bioconda-recipes

[mfansler]

The tag shows v1.0.0, but the DESCRIPTION file shows v0.1.0.

[brandon-hastings]

Of course, I will bump the version number and repackage

[mfansler]

Closing, since this is merged on Bioconda (bioconda/bioconda-recipes#55213).