Changes in version 1.0.5                        

  - Bug fix: if feature id - term id mapping is not unique (which can
    happen), features are duplicated in counting; fixed by
    dplyr::distinct() on mapping
  - Correction in vignette: using yeast genome for topGO, instead of
    human.
  - Improving test coverage
  - Making tests and examples resilient to Ensembl outage.

                        Changes in version 1.0.4                        

  - Reinstated Bioplanet access, this time with graceful fail when the
    website is down.
  - Minor code changes.

                        Changes in version 1.0.2                        

  - Bug fixes, examples need on_error = "warn"

                        Changes in version 1.0.1                        

  - First update after Bioconductor release
  - Implemented changes to prevent the package from build/check fail, if
    one of the remote servers is not responding
  - Moved from httr to httr2
  - Tests and examples now generate warnings in case of server failure
  - Added tests for behaviour in case of a non-responsive server
  - Extended test coverage to 100%, except for the interactive example

                       Changes in version 0.99.7                        

  - Minor changes to prepare for Bioconductor release
  - Reverting temporarily to readr version 1 to circumvent a vroom 1.6.4
    bug

                       Changes in version 0.99.6                        

In response to reviewer's comments

  - The wording in the vignette was adjusted to more clearly convey the
    purpose of the package to users
  - Rewritten the description in DESCRIPTION file to clearly convey the
    purpose of the package to users

BioPlanet seems defunct

  - Removed BioPlanet for good, as their webpage is continuously down
    and the maintainer is not responding

Minor adjustments to speed up building and testing

  - Removed KEGG from interactive example to speed up vignette building
    (GO and Reactome are sufficient for a simple example)
  - Replaced yeast with simpler organisms in Wiki and KEGG tests to
    speed up testing
  - Replaced yeast with simpler organisms in Wiki and KEGG examples to
    speed up checking

                       Changes in version 0.99.5                        

  - Major overhaul following comments from Bioconductor's reviewer.

                       Changes in version 0.99.4                        

  - Taking BiocCheck new warnings into account: adding @return to data
    roxygens.

                       Changes in version 0.99.3                        

  - Continuing issues with access to BioPlanet. fetch_bp example is now
    marked donotrun and testing fetch_bp is removed to ensure smooth
    build and check even when BioPlanet server is down.

                 Changes in version 0.99.2 (2023-05-24)                 

  - BioPlanet's tripod.nih.gov SSL certificate seems to be fixed, so
    reversing to the original read_csv code.

                 Changes in version 0.99.1 (2023-04-25)                 

  - BioPlanet database vanished from internet and there is no sign of it
    coming back. Removing all BioPlanet-related code and replacing
    BioPlanet with GO in the vignette and examples (this, alas, makes it
    longer to check).
  - OK, it is back, but I keep GO examples and vignettes.
  - Minor improvements to documentation.

                 Changes in version 0.99.0 (2023-04-20)                 

  - Pre-release Bioconductor version.

                 Changes in version 0.1.17 (2023-04-18)                 

  - New units tests added

                 Changes in version 0.1.16 (2023-03-16)                 

  - Added a fix to work correctly with integer feature IDs.

                 Changes in version 0.1.15 (2023-03-02)                 

  - Fixed a bug where there are some features at a term that are not
    present in the universe (all features). This could happen when the
    universe was particularly small. Potentially a serious bug.

                 Changes in version 0.1.14 (2023-02-02)                 

  - Ditched large and clunky Rfast and using native R environments as
    fast hashes (see
    https://riptutorial.com/r/example/18339/environments-as-hash-maps)
  - A few tweaks and improvements

                       Changes in version 0.1.13                        

  - Added functions get_term_features and get_feature_terms to access
    data safely
  - HACK: BioPlanet server's SSL certificate expired, so need insecure
    download.

                 Changes in version 0.1.11 (2022-10-11)                 

  - Significant speed-up of enrichment by using Rfast::Hash in place of
    R lists
  - KEGG improvements, recognizing flat file genes with no gene synonym
  - Additional tests for Reactome
  - Minor improvements and fixes

                 Changes in version 0.1.10 (2022-10-04)                 

  - Style changes for BiocCheck
  - Adding more tests
  - Fixing a bug in parse_kegg_genes

                 Changes in version 0.1.9 (2022-09-13)                  

  - Replacing ontologyIndex::get_ontology with a simpler parser
      - Replacing KEGGREST with own simple API parsers
      - Applying BiocStyle to the vignette
      - improving test_functional_enrichment

                 Changes in version 0.1.8 (2022-09-06)                  

  - fetch_reactome provides two ways of retrieving data, via one
    downloadable file or via APIs

                 Changes in version 0.1.7 (2022-09-01)                  

  - small fixes
  - link to a separate GitHub Shiny app added
  - added support for WikiPathways
  - improved robustness
  - more tests

                 Changes in version 0.1.6 (2022-08-23)                  

  - bug fix in fetch_kegg
  - removed min_count and fdr_limit arguments from
    functional_enrichment; filtering can be done afterwards
  - added a small Shiny app as an example of fenr
  - updates to vignette

                        Changes in version 0.1.5                        

  - added vignette
  - removeLazyData
  - DESCRIPTION updaates
  - replacing url_exists with RCurl::url.exists
  - added NEWS.md