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rinstallationlittler

how to install from bioconductor using install2.r from littler?

I'm trying to use https://cran.r-project.org/web/packages/littler/vignettes/littler-examples.html#install2r:_With_Cmdline_Parsing to install some packages during which I get the error dependency 'graph' is not available. It appears that this package is available from Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/graph.html) but I don't know how to install it using install2.r.

So, specifically how can I install bioconductor packages using install2.r?

Solution

  • You can't because BioConductor uses a different repository structure.

    But because this is a frequent-enough problem, I recently added a helper script installBioc.r you use. To use it, first do

     install.r littler BiocManager

    to make sure we have the current littler release as well as the BioC package BiocManager we need. Then use eg

      /usr/local/lib/R/site-library/littler/examples/installBioc.r S4Vectors

    and it will go off and install BiocVersion, S4Vectors as well as the dependency BiocGenerics.