- rename
OntologyandOntologiestoolsOntologyandolsOntologiesmethods/classes to avoid clashed with theAnnotationDbi::Ontologygeneric. Same for[ols]Termand[ols]Terms. Also rename[ols]Propert[y/ies]for consistency. - MS ontology not available anymore. Use GO term in
CVParamexamples and tests. - Fix bug in
[,,,]constructor, allowing commas in the term name.
- Typo and references in manual pages.
- Add orcid.
- Fix different URI locations (see #42)
- Fix logical syntax in url.
- Refactoring to use REST API for OLS4.
- REST queries now use httr2 instead of superseded
httr. - The term(s) and property constructors are capitalised as
Term(),Terms()andProperties().
- Fix unit tests.
- New devel version (Bioc 3.18)
- Fail with useful message when ols query can't be converted to terms.
- Fix error due to failing term().
- Fix failing unit test since change in GO.
- Fix new error when converting an Ontology to
data.frame.
- Fix error when converting term with missing slots to
data.frame.
- New devel version (Bioc 3.16)
- New release version (Bioc 3.15)
- Remove failing
CVParams()examples
- Don't show empty
termDesc(trm)in vignette.
- New devel version
- Fix failing unit test
- New devel version for Bioc 3.14
- Replace failing unit tests after GO:0032801 changed.
- Fix error for empty query results
- New as.data.frame OlsSearch S3 method
- Fix failing unit test (number of obsolete terms in
test_Terms.R)
- Fix pagination of ebi.ac.uk results contributed by Andrew Clugston (AndrewC160) - see issue #27.
- For failing unit test (number of obsolete terms in
test_Terms.R)
- Fix failing unit test <2020-08-26 Wed>
- Fix failing unit test (Matched error messsage changed) <2020-07-01 Wed>
- Fix failing unit test (Terms changed) <2020-06-09 Tue>
- Fix failing unit test (GO description changed) <2020-05-01 Fri>
- Bioconductor devel version (Bioc 3.12)
- Bioconductor release version (Bioc 3.11)
- Bioconductor version bump
- Remove failing test - term is now obsolete <2019-10-12 sam.>
- Fix failing test <2019-08-12 Mon>
- Fix failing test <2019-04-16 Tue>
- Add ImmunoOncology biocView
- New version for Bioc 3.9 (devel)
- New version for Bioc 3.8 (release)
- Fix unit test <2018-10-06 Sat>
- Update news and pkgdown
- replace BiocInstaller biocLite mentions with BiocManager
- Fix bug ancestors function, reported by Christian Holland (see #26 for details) <2018-06-01 Fri>
- Bioconductor devel
- Bioconductor release
- Nothing yet
- Fix failing partOf unit test <2017-11-27 Mon>
- Bioconductor devel 3.7
- Bioconductor release 3.6
- bump version
- Fix failing test do to different order <2017-10-23 Mon>
- Fix bug in pagesize limit when reporting children, ancestors, ... (see issue #25) <2017-10-17 Tue>
- New term(s) to data.frame coersion methods <2017-10-14 Sat>
- Add import Ontology in NAMESPACE
- Update to latest BiocStyle <2017-09-01 Fri>
- Quick fix for issue #24 (reported upsteams) <2017-09-02 Sat>
- Use Ontology generic from BiocGenerics <2017-09-03 Sun>
- Fix unit test <2017-06-20 Tue>
- Bioconductor devel 3.6
- Bioconductor release 3.5
- Fix failing test <2017-03-15 Wed>
- Ammend failing Ontologies unit test (related to changes made in version 2.3.3: the GO name reverted back to Gene Ontolgy) <2017-01-11 Wed>
- Add ctb to Authors@R <2016-12-28 Wed>
- use NEWS.md <2016-12-28 Wed>
- Ammend failing Ontologies unit test <2017-01-02 Mon>
- Update test to reflect GO's new title <2016-12-21 Wed>
- Fix failing unit test <2016-11-22 Tue>
- Bioconductor devel 3.5
- Bioconductor release 3.4
- Fix failing tests <2016-09-16 Fri>
- Explicitly extract raw content to fix error <2016-04-02 Sat>
- Using the REST API
- Package deprecation message <2015-12-30 Wed>
- Bioc devel 3.3
- Bio release 3.2
- fix failing unit tests <2015-07-02 Thu>
- add test script <2015-06-30 Tue>
- more unit tests <2015-06-30 Tue>
- Fix bug in as("[MS, MS:123, ]", "CVParam") and add unit test <2015-06-19 Fri>
- New charIsCVParam function to check if a character represents a valid CV param <2015-06-16 Tue>
- Unit test <2015-06-15 Mon>
- New char to CVParam coerce method <2015-06-15 Mon>
- Bioc devel 3.2
- Bioc release 3.1
- Removing (temporarily) allIds("GO")) example as currently returns illegal message to fix testing error [2014-10-07 Tue]
- Updating roxygem inline docs to fix errors in generated Rds [2014-10-07 Tue]
- add utils to Imports [2014-04-28 Mon]
- new devel, Bioc 3.0
- release for Bioc 2.14
- pretty printing with strwrap(mtd[...]) in vignette and termMetadata S3 printing method for readable-utput (suggestion from Martin Morgan) [2014-02-18 Tue]
- Using BiocStyle vignette [2014-02-18 Tue]
- split go terms (PRO:...) instead-f ids (PR:...) in vignette tgnqueryShow chunk <2013-10-19 Sat>
- new devel for Bioc 2.14
- fixed bug in isIdObsolete, reported by Alex Thomas <2013-07-27 Sat>
--ther example in CVParam-class example, as PSI-ntology is not available <2013-05-02 Thu>
Changes IN VERSION 1.3.0
- Bioc 2.13 devel version bump
- Bioc 2.12 stable version bump
- Using knitr as VignetteEngine and visual tweaking <2013-02-17 Sun>
- update vignette for knitr 1.0 compatibility, based-n Dan's updates in stable version <2013-01-15 Tue>
- changed query to avoid failure (see issue #6) <2012-12-26 Wed>
- added missing space in
Empty query results after 3attempts<2012-12-26 Wed>
- updated-lsQuery example <2012-12-25 Tue>
- .rolsEnv now has emptyenv() as parent <2012-10-31 Wed>
- fixing vignette <2012-10-02 Tue>
- new iface <2012-10-02 Tue>
- version bump for next devel <2012-10-01 Mon>
o updated README.md (for github) and .Rbuildignore <2012-09-19 Wed>
o updated biocViews <2012-09-18 Tue>
o using knitr instead-f pgfSweave <2012-08-13 Mon>
- fixed-lsQuery issued warning when missing(ontologyNames) irrespective-f extact <2012-05-22 Tue>
- really using pdfSweave <2012-05-18 Fri>
- using pdfSweave <2012-05-16 Wed>
- changed VignetteIndexEntry <2012-05-16 Wed>
- removed roxygen2 from Suggests <2012-05-16 Wed>
- added README file describinh Rd generation with roxygen2 <2012-05-16 Wed>
- implementing Mark Carlson's suggestions
- (Temporarily) removing pgf <2012-05-15 Tue>
- added Collate field <2012-05-15 Tue>
- moving generics and class definitions to AllGenerics.R and AllClasses.R <2012-05-15 Tue> --lsQuery now repeats query 'n' times if reply is empty - see man page for a brief discussion <2012-05-15 Tue>
- updated vignette to discuss-ff/on-line data access <2012-05-15 Tue>
- downgraded SSOAP dependency to (>= 0.8.0), as later SSOAP versions are not available through biocLite (due to check errors). rols works with SSOAP 0.8.0 and XMLSchema 0.7.2. <2012-05-11 Fri>
- added url to DESCRIPTION <2012-05-11 Fri>
- released CVParam validity contrains: now CVParam name must match term-r any synonym <2012-05-11 Fri>
- new CVParam constructor <2012-05-11 Fri>
- minor vignette update <2012-05-04 Fri>
- new CVParam class <2012-05-08 Tue>
- More verbose CVParam validity error msg <2012-05-08 Tue>
- new 'rep' method for CVParam <2012-05-09 Wed>
--lsQuery has a new 'exact' parameter <2012-05-04 Fri>
- import(XMLSchema) to remove warning at startup <2012-05-04 Fri>
- vignette update <2012-04-30 Mon>
- added GO.db to Suggests for vignette <2012-04-30 Mon>
- bumped version to 0.99 for Bioc submission <2012-04-30 Mon>
- added a vignette <2011-12-18 Sun>
- added xtable in suggests for vignette <2011-12-18 Sun>
- added parents() and childrenRelations() query functions <2011-12-18 Sun>
- added specific SSOAP and XMLSchema version requirements <2011-12-18 Sun>
- fixed a couple-f typos <2011-12-18 Sun>
- initial release