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AliYoussef96 / LimROTS

A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Analysis of Proteomics and Metabolomics Data
https://aliyoussef96.github.io/LimROTS/
Artistic License 2.0
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vignettes/ #12

Closed antagomir closed 2 weeks ago

antagomir commented 1 month ago

The vignettes/ R file might be better to remove from github repo, just keep the qmd file.

AliYoussef96 commented 1 month ago

The vignettes now contain two files: an Rmd and a Qmd. Qmd file only, raises an error in BiocCheck.

I have a question regarding the vignettes. I know that using eval=FALSE is against Bioconductor guidelines, but I can't think of another way to handle it. We have six examples, each with two functions running in parallel processing, and it takes 3-5 minutes to run each function.

antagomir commented 1 month ago

Ok interesting - then you can just keep the Rmd. I think Bioc has preparations ongoing to support Qmd but perhaps that is not ready yet then.

antagomir commented 1 month ago

What is the problem where you need eval=FALSE? Just the speed, or also something else? State the actual problem so it is easier to comment on possible solutions.

AliYoussef96 commented 1 month ago

Yes just the speed

antagomir commented 4 weeks ago

Any chance to make the examples more light-weight? Then you would not need to disable them. It is rather useful to have these for continuous testing.

AliYoussef96 commented 3 weeks ago

Hi, The only way to reduce the examples' runtime is to select just one example, as CRAN does not allow more than 2 cores to be used during the check process. I already did that, and now it takes around 3 minutes to run the CRAN check.