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NEWS.md

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Version 0.1.5

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

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

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

Version 0.1.8 (2022-09-06)

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

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

Version 0.1.10 (2022-10-04)

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

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

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.

Version 0.1.14 (2023-02-02)

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.

Version 0.1.16 (2023-03-16)

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

Version 0.1.17 (2023-04-18)

  • New units tests added

Version 0.99.0 (2023-04-20)

  • Pre-release Bioconductor version.

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.

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.

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.

Version 0.99.4

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

Version 0.99.5

  • Major overhaul following comments from Bioconductor's reviewer.

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

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

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

Version 1.0.2

  • Bug fixes, examples need on_error = "warn"

Version 1.0.4

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

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

Version 1.0.6

  • Changed the Ensembl mapping file downloaded from Reactome to "Physical entity" mapping, as it contains gene symbols, in addition to the Ensembl IDs.
  • Changed the name of GAF column DB Object Synonym from gene_synonym to gene_id for consistency with other methods.
  • Corrected Reactome test as it failed with multiple gene symbols per gene id.
  • Replaced biomaRt with a single RESTful XML call; as biomaRt is used only once to obtain GO terms, this replacement reduced dependency footprint of the package

Version 1.0.7

  • Improved error handling with unresponsive servers - timeouts are now handled gracefully

Version 1.0.8

  • Further improving error handling, making sure assert_url_path() handles timeouts properly
  • Introduced on_error = "ignore" for test purposes

Version 1.0.9

  • Changed the way assert_url_path() handles some remote files - it turns out every time it was called, the entire file was unnecessary downloaded, leading to duplication. Now we only assert top directories. Should speed things up!
  • Increased default timeout to 30 s.

Version 1.0.10

  • Due to recurring issues with build and check on Bioconductor's machines, I have removed all database downloads from the vignette. Any glitch in the GO server, or simply an internet problem would cause the vignette build to crash. The GO-term information is now attached as data and loaded in the vignette.
  • Made sure the package passes BUILD and CHECK with no internet connection.
  • Correction in vignette: using yeast genome for topGO, instead of human (somehow it was not applied in 1.0.5).

Version 1.2.1

  • Go term namespace added to the information extracted by fetch_go.

Version 1.4.1

  • Attempted to fix a bizarre error message on Bioconductor's test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error vector memory limit of 64.0 Gb reached, see mem.maxVSize() happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.