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NEWS.md

NEWS.md
In lgatto/rols: An R interface to the Ontology Lookup Service

rols 2.99

rename Ontology and Ontologies to olsOntology and olsOntologies methods/classes to avoid clashed with the AnnotationDbi::Ontology generic. Same for [ols]Term and [ols]Terms. Also rename [ols]Propert[y/ies] for consistency.
MS ontology not available anymore. Use GO term in CVParam examples 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REST queries now use httr2 instead of superseded httr.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() and Properties().

rols 2.29

Fix unit tests.

New devel version (Bioc 3.18)

rols 2.25

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)

rols 2.24

New release version (Bioc 3.15)

rols 2.23

Remove failing CVParams() examples

Don't show empty termDesc(trm) in vignette.

New devel version

rols 2.21

Fix failing unit test

New devel version for Bioc 3.14

rols 2.19

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)

rols 2.17

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)

rols 2.16

Bioconductor release version (Bioc 3.11)

rols 2.15

Bioconductor version bump

rols 2.13

Remove failing test - term is now obsolete <2019-10-12 sam.>

Fix failing test <2019-08-12 Mon>

rols 2.11

Fix failing test <2019-04-16 Tue>

Add ImmunoOncology biocView

New version for Bioc 3.9 (devel)

rols 2.10

New version for Bioc 3.8 (release)

rols 2.9

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 https://github.com/lgatto/rols/issues/26 for details) <2018-06-01 Fri>

Bioconductor devel

rols 2.8

Bioconductor release

rols 2.7

Nothing yet

Fix failing partOf unit test <2017-11-27 Mon>

Bioconductor devel 3.7

rols 2.6

Bioconductor release 3.6

rols 2.5

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

rols 2.4

Bioconductor release 3.5

rols 2.3

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

rols 2.2

Bioconductor release 3.4

Fix failing tests <2016-09-16 Fri>

rols 1.99

Explicitly extract raw content to fix error <2016-04-02 Sat>

Using the REST API

rols 1.13

Package deprecation message <2015-12-30 Wed>

Bioc devel 3.3

rols 1.12

Bio release 3.2

rols 1.11

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>

rols 1.10

Bioc devel 3.2

Bioc release 3.1

rols 1.7

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

rols 1.6

release for Bioc 2.14

rols 1.5

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

rols 1.3

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

rols 1.2

Bioc 2.12 stable version bump

rols 1.1

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>

rols 0.99

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>

rols 0.2

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

lgatto/rols documentation built on April 29, 2024, 12:20 p.m.

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lgatto/rols An R interface to the Ontology Lookup Service

NEWS.md In lgatto/rols: An R interface to the Ontology Lookup Service

rols 2.99

CHANGES IN VERSION 2.99.5

CHANGES IN VERSION 2.99.4

CHANGES IN VERSION 2.99.3

CHANGES IN VERSION 2.99.2

CHANGES IN VERSION 2.99.1

CHANGES IN VERSION 2.99.0

rols 2.29

CHANGES IN VERSION 2.29.1

CHANGES IN VERSION 2.29.0

rols 2.25

CHANGES IN VERSION 2.25.5

CHANGES IN VERSION 2.25.4

CHANGES IN VERSION 2.25.3

CHANGES IN VERSION 2.25.2

CHANGES IN VERSION 2.25.1

CHANGES IN VERSION 2.25.0

rols 2.24

CHANGES IN VERSION 2.24.0

rols 2.23

CHANGES IN VERSION 2.23.2

CHANGES IN VERSION 2.23.1

CHANGES IN VERSION 2.23.0

rols 2.21

CHANGES IN VERSION 2.21.1

CHANGES IN VERSION 2.21.0

rols 2.19

CHANGES IN VERSION 2.19.4

CHANGES IN VERSION 2.19.3

CHANGES IN VERSION 2.19.2

CHANGES IN VERSION 2.19.1

rols 2.17

CHANGES IN VERSION 2.17.4

CHANGES IN VERSION 2.17.3

CHANGES IN VERSION 2.17.2

CHANGES IN VERSION 2.17.1

CHANGES IN VERSION 2.17.0

rols 2.16

CHANGES IN VERSION 2.16.0

rols 2.15

CHANGES IN VERSION 2.15.0

rols 2.13

CHANGES IN VERSION 2.13.2

CHANGES IN VERSION 2.13.1

rols 2.11

CHANGES IN VERSION 2.11.2

CHANGES IN VERSION 2.11.1

CHANGES IN VERSION 2.11.0

rols 2.10

CHANGES IN VERSION 2.10.0

rols 2.9

CHANGES IN VERSION 2.9.4

CHANGES IN VERSION 2.9.3

CHANGES IN VERSION 2.9.2

CHANGES IN VERSION 2.9.1

CHANGES IN VERSION 2.9.0

rols 2.8

CHANGES IN VERSION 2.8.0

rols 2.7

CHANGES IN VERSION 2.7.2

CHANGES IN VERSION 2.7.1

CHANGES IN VERSION 2.7.0

rols 2.6

CHANGES IN VERSION 2.6.0

rols 2.5

CHANGES IN VERSION 2.5.6

CHANGES IN VERSION 2.5.5

CHANGES IN VERSION 2.5.4

CHANGES IN VERSION 2.5.4

CHANGES IN VERSION 2.5.3

CHANGES IN VERSION 2.5.2

CHANGES IN VERSION 2.5.1

CHANGES IN VERSION 2.5.0

rols 2.4

CHANGES IN VERSION 2.4.0

rols 2.3

CHANGES IN VERSION 2.3.5

CHANGES IN VERSION 2.3.4

lgatto/rols
An R interface to the Ontology Lookup Service

NEWS.md
In lgatto/rols: An R interface to the Ontology Lookup Service