## 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) - 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 ## 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. ## Version 1.4.2 - Added evidence code column to GO-term mapping table. It can be used to filter mapping based on their quality. See https://geneontology.org/docs/guide-go-evidence-codes for explanation.