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rformassspectrometry / MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.
https://rformassspectrometry.github.io/MetaboAnnotation/
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packages for function validateMatchedSpectra #78

Closed chufz closed 2 years ago

chufz commented 2 years ago

Currently, the packages 'shiny', 'shinyjs', 'DT' and 'plotly' are not installed with MetaboAnnotation, but are required for the validateMatchedSpectra function. Should these dependencies be included or is there a reason to keep them separate?

jorainer commented 2 years ago

If possible I would like to keep them separate. These will only be needed for this one function and we shouldn't require all package users to depend on all these packages if they are just using the core functionality of the package. Keeps the package dependency low and easier to maintain.

We do a similar thing in Spectra: the HDF5 functionality and mzR/proteowizard are not required packages. They are suggested. This saves us from potential installation problems with these packages (that can happen on some platforms/compiler versions).

jorainer commented 2 years ago

And note that also suggested packages could be automatically installed with:

BiocManager::install("MetaboAnnotation", dependencies = c("Depends", "Imports", "Suggests"))