Recommended logging/logger for bioconductor package submission.
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@cff7e13e
Last seen 4 months ago
United States

What R logging/logger package are we recommend to use for packages submitted to bioconductor? I could not find package guidance on this. I would prefer to have a debug log level to aid in my development of a regression package I am working on submitting.

  1. Unfortunately, there is no standard logger in R. Is there a logger recommended by bioconductor? Here are some common R logger packages: https://stackoverflow.com/a/39129581/9100276

  2. Perhaps the answer is, 'you should not be using any logger'. In which case I would be interested in the reasoning.

  3. Perhaps the answer is, 'you should write your own logger in R or C/C++'. In which case I would be interested in the reasoning.

Simply describing how many/most bioconductor packages handle logging will suffice.

Thank you for your time and guidance,

– Matthew Hamilton

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I'm not aware of many packages in R using loggers, but you can use any of the list as long as the Bioconductor checks (mainly BiocCheck) passes without notes. You can use debug or browser to interactively explore the state of the variables during the evaluation of a function, which sometimes is simpler and as useful as a logger.

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