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SomaLogic / SomaDataIO

The SomaDataIO package loads and exports 'SomaScan' data via the 'SomaLogic Operating Co., Inc.' proprietary data file, called an ADAT ('*.adat'). The package also exports auxiliary functions for manipulating, wrangling, and extracting relevant information from an ADAT object once in memory.
https://somalogic.github.io/SomaDataIO/
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SomaDataIO on CRAN / Bioconductor #20

Closed lassemaretty closed 1 year ago

lassemaretty commented 2 years ago

Hi,

We are working on an R package for performing analyses of SomaLogic data and use the SomaLogicIO package to read .adat files etc. As we want to submit our package to CRAN, it seems we also need any dependencies to be on CRAN or Bioconductor. Hence, we currently need to copy the necessary SomaDataIO files into our repository, but it would be more clean and future proof to be able to depend directly on your package.

Do you have any plans for submitting your package to any of these repositories?

Best regards,

Lasse Maretty

stufield commented 2 years ago

HI @lassemaretty,

Thank you for your question. Yes, indeed this is something we have thought about at length since we published SomaDataIO here on GitHub. There are some pros/cons to consider before that happens (but it is on our radar!). We actually have a coming meeting next week, at which I'll bring it up and get back to you.

Thanks again! Cheers,

lassemaretty commented 2 years ago

Hi @stufield,

Sorry for my late reply - I was on holiday:)

Sounds great if you are considering putting it on CRAN, we would really appreciate that. Please let me know of any developments in this direction.

Thanks! Best, Lasse

stufield commented 2 years ago

Hi @lassemaretty ,

Good news! The plan is to eventually submit to CRAN, which would enable you to submit your package to CRAN with a SomaDataIO dependency. However, I the timeline for this may be limiting. There are still remaining issues that would need to be ironed out before we can finalize a submission to CRAN, e.g. marketing, branding, re-naming, etc. (there is a possibility that SomaDataIO will be renamed as part of a broader branding exercise at SomaLogic). My best estimate for a CRAN submission is the 1-3 month time frame.

If this fits within your time limitations, fantastic. If not, it might be possible to "borrow" our code internally under the MIT license until SomaDataIO is officially on CRAN. This would enable you to move forward with your package, and only require a small refactoring to add the dependency once SomaDataIO is available on CRAN. If you go this route, I would be happy to help if you let me know which part of SomaDataIO you depend upon.

Cheers, Stu

lassemaretty commented 2 years ago

Hi @stufield

Sounds great that you are planning on a CRAN submission. It would enable us to create a nice ecosystem around SomaLogic data. Timeframe is not critical as we have now adopted a workaround that will do for now.

I look forward to seeing it on CRAN.

Thanks again,

Lasse

lassemaretty commented 1 year ago

Hi @stufield

Just kindly curious about whether there has been any progress towards a CRAN or bioconductor submission?

Best,

Lasse

stufield commented 1 year ago

Hi @lassemaretty ,

We've targeted CRAN submission for an end Jan - early Feb 2023 timeframe. I'll be working with the marketing team in the coming weeks to finalize a possible name change of the package to align with our other open source software offerings. So please be aware of that ... new branding, new name, new v1.0.0 versioning, etc. All those decisions are the major roadblocks at the moment. Once they're clear, I imagine a submission and acceptance will be relatively straightforward.

Thanks! Stu

lassemaretty commented 1 year ago

Hi Stu,

Thank you for your response! Great to hear that this is still in the making. I look forward to seeing it on CRAN!

Best,

Lasse

stufield commented 1 year ago

Submitted to CRAN 🤞🏽

stufield commented 1 year ago

Accepted and published!

https://cran.r-project.org/web/packages/SomaDataIO/index.html

lassemaretty commented 1 year ago

Congrats! Thank you for this effort.

Best,

Lasse

tir. 21. mar. 2023 kl. 18.12 skrev Stu Field @.***>:

Accepted and published!

https://cran.r-project.org/web/packages/SomaDataIO/index.html

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