NEWS
fenr 1.2.1
- Go term namespace added to the information extracted by
fetch_go.
fenr 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).
fenr 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.
fenr 1.0.8
- Further improving error handling, making sure
assert_url_path() handles timeouts properly
- Introduced on_error = "ignore" for test purposes
fenr 1.0.7
- Improved error handling with unresponsive servers - timeouts are now handled gracefully
fenr 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
fenr 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
fenr 1.0.4
- Reinstated Bioplanet access, this time with graceful fail when the website is down.
- Minor code changes.
fenr 1.0.2
- Bug fixes, examples need on_error = "warn"
fenr 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
fenr 0.99.7
- Minor changes to prepare for Bioconductor release
- Reverting temporarily to readr version 1 to circumvent a vroom 1.6.4 bug
fenr 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
fenr 0.99.5
- Major overhaul following comments from Bioconductor's reviewer.
fenr 0.99.4
- Taking
BiocCheck new warnings into account: adding @return to data roxygens.
fenr 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.
fenr 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.
fenr 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.
fenr 0.99.0 (2023-04-20)
- Pre-release Bioconductor version.
fenr 0.1.17 (2023-04-18)
fenr 0.1.16 (2023-03-16)
- Added a fix to work correctly with integer feature IDs.
fenr 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.
fenr 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
fenr 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.
fenr 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
fenr 0.1.10 (2022-10-04)
- Style changes for BiocCheck
- Adding more tests
- Fixing a bug in
parse_kegg_genes
fenr 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
fenr 0.1.8 (2022-09-06)
fetch_reactome provides two ways of retrieving data, via one downloadable file or via APIs
fenr 0.1.7 (2022-09-01)
- small fixes
- link to a separate GitHub Shiny app added
- added support for WikiPathways
- improved robustness
- more tests
fenr 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
fenr 0.1.5
- added vignette
- removeLazyData
- DESCRIPTION updaates
- replacing url_exists with RCurl::url.exists
- added NEWS.md