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MD-Anderson-Bioinformatics / NGCHM-R

An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
http://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview
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Pkgdown Updates #42

Closed marohrdanz closed 7 months ago

marohrdanz commented 7 months ago

This pull request addresses issues building the pkgdown website from merging Pull Request #41 .

I used my fork of this repo to test and resolve the following issues:

  1. Build failure: unable to install NGCHMDemoData and NGCHMSupportFiles
    • pkgdown does not recognize 'Additional_repositories' from the DESCRIPTION file
    • resolution: add the r-universe repo in the pgkdown workflow file (ca9c4ef)
  2. Build failure: Java version errors
    • The default version of java is 8, resulting in errors such as: 
        Exception in thread "main" java.lang.UnsupportedClassVersionError:
  mda/ngchm/datagenerator/ShaidyRMapGen has been compiled by a more
  recent version of the Java Runtime (class file version 55.0), this
  version of the Java Runtime only recognizes class file versions up
  to 52.0
    • resolution: install java 11 in the workflow (73f9c0e)

Additional changes:

  1. Updated documentation to direct users to install:
    • tsvio from CRAN
    • NGCHMSupportFiles from r-universe
    • NGCHMDemoData from r-universe
    • NGCHM from r-universe (we had been instructing users to use remotes::install_github()) (2e23b86)