[Bioc-devel] d3heatmap dependency error

[Martin Morgan]

If the package is deprecated on CRAN, that means that it fails to pass the CRAN checks and the author has not updated the code. It is, in this sense, 'broken', and there is no value for our users to enabling access to broken packages.

The options for you are to:

  - Ensure (e.g., by contacting the maintainer) that d3heatmap is updated to once again pass CRAN checks

  - Modify your code to no longer depend on d3heatmap. A common conversation recently has been careful choice of dependencies and the functionality that the dependency provides relative to the contribution of your package -- if you are contributing a novel statistical method, maybe the goal should be to implement the method and return an object that is amenable to effective visualization, rather than to impose a visualization on the user? 

  - Decide that d3heatmap is essential to your package, and without d3heatmap your package has no added value. As such, your package should be deprecated and removed from Bioconductor (this is what will happen by default, if your package continues to depend on a package that is not available in CRAN).

Martin


On 7/11/20, 9:22 PM, "Bioc-devel on behalf of S Manimaran" <bioc-devel-bounces using r-project.org on behalf of manimaran_1975 using hotmail.com> wrote:

    Hi,

    I have a package that depends on d3heatmap. Apparently d3heatmap is no longer maintained and removed from CRAN repository.

    Now, I am getting the following error when installing my package.
    ERROR: dependency 'd3heatmap' is not available

    https://cran.r-project.org/web/packages/d3heatmap/index.html
    Package 'd3heatmap' was removed from the CRAN repository.
    Formerly available versions can be obtained from the archive.
    https://cran.r-project.org/src/contrib/Archive/d3heatmap/

    I am still able to install the last version from the archive.

    require(devtools)
    install_version("d3heatmap", version = "0.6.1.2")

    Is there a way to make the Bioconductor use the archived version without giving the error? Or is the only solution is to rewrite my package without d3heatmap? Or is there an easy alternative to d3heatmap?

    Thanks,
    Mani

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