Changes in 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.
Changes in 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.
Changes in version 1.2.1
- Go term namespace added to the information extracted by fetch_go.
Changes in 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).
Changes in 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.
Changes in version 1.0.8
- Further improving error handling, making sure assert_url_path()
handles timeouts properly
- Introduced on_error = "ignore" for test purposes
Changes in version 1.0.7
- Improved error handling with unresponsive servers - timeouts are now
handled gracefully
Changes in 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
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
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