Changelog • rols

rols 3.9.3

Point URL and BugReports at the current repository and documentation site. The previous URL no longer resolved.
Stop excluding NEWS.md from the built package, so that package news is picked up for the Bioconductor release announcements.

rols 3.9.2

Remove the startup deprecation warning, left over from before the package was transferred.
olsTerm() now looks terms up by their identifier instead of reconstructing their IRI from the ontology’s fileLocation. The latter only handled ontologies served from the EBI and OBO PURL servers, and failed with “Unknown fileLocation” for 75 of the 283 ontologies in OLS4.
Terms are no longer rejected as invalid when OLS4 omits an empty field (such as ontology_prefix) from its response; the corresponding slot is set to NA instead.
Drop the 1000 row cap in OlsSearch(). OLS3 enforced it server-side, OLS4 does not, and it was applied to the rows slot but not to the query URL, leaving the two out of sync.
Fix the OlsSearch() example, which failed R CMD check when rbind()-ing pages of search results that had different columns (contributed by Levi Waldron, lwaldron, in #52).
Document that OLS4 omits empty fields from search responses, so the columns of a coerced data.frame vary between queries.
Use https rather than http for the search and properties endpoints.

rols 3.9.1

Transfer package and maintenance to Sehyun Oh (shbrief). Thank you for taking the package over!

rols 3.7.1

Fix bug in rols::Ontologies() (see #48)

CHANGES IN VERSION 2.99.5

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.

CHANGES IN VERSION 2.99.4

Typo and references in manual pages.

CHANGES IN VERSION 2.99.3

Add orcid.

CHANGES IN VERSION 2.99.2

Fix different URI locations (see #42)

CHANGES IN VERSION 2.99.1

Fix logical syntax in url.

CHANGES IN VERSION 2.99.0

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REST queries now use httr2 instead of superseded httr.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().

CHANGES IN VERSION 2.29.1

Fix unit tests.

CHANGES IN VERSION 2.29.0

New devel version (Bioc 3.18)

CHANGES IN VERSION 2.25.5

Fail with useful message when ols query can’t be converted to terms.

CHANGES IN VERSION 2.25.4

Fix error due to failing term().

CHANGES IN VERSION 2.25.3

Fix failing unit test since change in GO.

CHANGES IN VERSION 2.25.2

Fix new error when converting an Ontology to data.frame.

CHANGES IN VERSION 2.25.1

Fix error when converting term with missing slots to data.frame.

CHANGES IN VERSION 2.25.0

New devel version (Bioc 3.16)

CHANGES IN VERSION 2.24.0

New release version (Bioc 3.15)

CHANGES IN VERSION 2.23.2

Remove failing CVParams() examples

CHANGES IN VERSION 2.23.1

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

CHANGES IN VERSION 2.23.0

New devel version

CHANGES IN VERSION 2.21.1

Fix failing unit test

CHANGES IN VERSION 2.21.0

New devel version for Bioc 3.14

CHANGES IN VERSION 2.19.4

Replace failing unit tests after GO:0032801 changed.

CHANGES IN VERSION 2.19.3

Fix error for empty query results
New as.data.frame OlsSearch S3 method

CHANGES IN VERSION 2.19.2

Fix failing unit test (number of obsolete terms in test_Terms.R)

CHANGES IN VERSION 2.19.1

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)

CHANGES IN VERSION 2.17.4

Fix failing unit test <2020-08-26 Wed>

CHANGES IN VERSION 2.17.3

Fix failing unit test (Matched error messsage changed) <2020-07-01 Wed>

CHANGES IN VERSION 2.17.2

Fix failing unit test (Terms changed) <2020-06-09 Tue>

CHANGES IN VERSION 2.17.1

Fix failing unit test (GO description changed) <2020-05-01 Fri>

CHANGES IN VERSION 2.17.0

Bioconductor devel version (Bioc 3.12)

CHANGES IN VERSION 2.16.0

Bioconductor release version (Bioc 3.11)

CHANGES IN VERSION 2.15.0

Bioconductor version bump

CHANGES IN VERSION 2.13.2

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

CHANGES IN VERSION 2.13.1

Fix failing test <2019-08-12 Mon>

CHANGES IN VERSION 2.11.2

Fix failing test <2019-04-16 Tue>

CHANGES IN VERSION 2.11.1

Add ImmunoOncology biocView

CHANGES IN VERSION 2.11.0

New version for Bioc 3.9 (devel)

CHANGES IN VERSION 2.10.0

New version for Bioc 3.8 (release)

CHANGES IN VERSION 2.9.4

Fix unit test <2018-10-06 Sat>

CHANGES IN VERSION 2.9.3

Update news and pkgdown

CHANGES IN VERSION 2.9.2

replace BiocInstaller biocLite mentions with BiocManager

CHANGES IN VERSION 2.9.1

Fix bug ancestors function, reported by Christian Holland (see https://github.com/lgatto/rols/issues/26 for details) <2018-06-01 Fri>

CHANGES IN VERSION 2.9.0

Bioconductor devel

CHANGES IN VERSION 2.8.0

Bioconductor release

CHANGES IN VERSION 2.7.2

Nothing yet

CHANGES IN VERSION 2.7.1

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

CHANGES IN VERSION 2.7.0

Bioconductor devel 3.7

CHANGES IN VERSION 2.6.0

Bioconductor release 3.6

CHANGES IN VERSION 2.5.6

bump version

CHANGES IN VERSION 2.5.5

Fix failing test do to different order <2017-10-23 Mon>

CHANGES IN VERSION 2.5.4

Fix bug in pagesize limit when reporting children, ancestors, … (see issue #25) <2017-10-17 Tue>

CHANGES IN VERSION 2.5.4

New term(s) to data.frame coersion methods <2017-10-14 Sat>

CHANGES IN VERSION 2.5.3

Add import Ontology in NAMESPACE

CHANGES IN VERSION 2.5.2

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>

CHANGES IN VERSION 2.5.1

Fix unit test <2017-06-20 Tue>

CHANGES IN VERSION 2.5.0

Bioconductor devel 3.6

CHANGES IN VERSION 2.4.0

Bioconductor release 3.5

CHANGES IN VERSION 2.3.5

Fix failing test <2017-03-15 Wed>

CHANGES IN VERSION 2.3.4

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>

CHANGES IN VERSION 2.3.3

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>

CHANGES IN VERSION 2.3.2

Update test to reflect GO’s new title <2016-12-21 Wed>

CHANGES IN VERSION 2.3.1

Fix failing unit test <2016-11-22 Tue>

CHANGES IN VERSION 2.3.0

Bioconductor devel 3.5

CHANGES IN VERSION 2.2.0

Bioconductor release 3.4

CHANGES IN VERSION 2.1.3

Fix failing tests <2016-09-16 Fri>

CHANGES IN VERSION 1.99.1

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

CHANGES IN VERSION 1.99.0

Using the REST API

CHANGES IN VERSION 1.13.1

Package deprecation message <2015-12-30 Wed>

CHANGES IN VERSION 1.13.0

Bioc devel 3.3

CHANGES IN VERSION 1.12.0

Bio release 3.2

CHANGES IN VERSION 1.11.6

fix failing unit tests <2015-07-02 Thu>

CHANGES IN VERSION 1.11.5

add test script <2015-06-30 Tue>
more unit tests <2015-06-30 Tue>

CHANGES IN VERSION 1.11.4

Fix bug in as(“[MS, MS:123, ]”, “CVParam”) and add unit test <2015-06-19 Fri>

CHANGES IN VERSION 1.11.3

New charIsCVParam function to check if a character represents a valid CV param <2015-06-16 Tue>

CHANGES IN VERSION 1.11.2

Unit test <2015-06-15 Mon>

CHANGES IN VERSION 1.11.1

New char to CVParam coerce method <2015-06-15 Mon>

CHANGES IN VERSION 1.11.0

Bioc devel 3.2

CHANGES IN VERSION 1.10.0

Bioc release 3.1

CHANGES IN VERSION 1.7.2

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]

CHANGES IN VERSION 1.7.1

add utils to Imports [2014-04-28 Mon]

CHANGES IN VERSION 1.7.0

new devel, Bioc 3.0

CHANGES IN VERSION 1.6.0

release for Bioc 2.14

CHANGES IN VERSION 1.5.2

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]

CHANGES IN VERSION 1.5.1

split go terms (PRO:…) instead-f ids (PR:…) in vignette tgnqueryShow chunk <2013-10-19 Sat>

CHANGES IN VERSION 1.5.0

new devel for Bioc 2.14

CHANGES IN VERSION 1.3.2

fixed bug in isIdObsolete, reported by Alex Thomas <2013-07-27 Sat>

CHANGES IN VERSION 1.3.1

–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

CHANGES IN VERSION 1.2.0

Bioc 2.12 stable version bump

CHANGES IN VERSION 1.1.6

Using knitr as VignetteEngine and visual tweaking <2013-02-17 Sun>

CHANGES IN VERSION 1.1.5

update vignette for knitr 1.0 compatibility, based-n Dan’s updates in stable version <2013-01-15 Tue>

CHANGES IN VERSION 1.1.4

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>

CHANGES IN VERSION 1.1.3

updated-lsQuery example <2012-12-25 Tue>

CHANGES IN VERSION 1.1.2

.rolsEnv now has emptyenv() as parent <2012-10-31 Wed>

CHANGES IN VERSION 1.1.1

fixing vignette <2012-10-02 Tue>
new iface <2012-10-02 Tue>

CHANGES IN VERSION 1.1.0

version bump for next devel <2012-10-01 Mon>

CHANGES IN VERSION 0.99.12

o updated README.md (for github) and .Rbuildignore <2012-09-19 Wed>

CHANGES IN VERSION 0.99.11

o updated biocViews <2012-09-18 Tue>

CHANGES IN VERSION 0.99.10

o using knitr instead-f pgfSweave <2012-08-13 Mon>

CHANGES IN VERSION 0.99.9

fixed-lsQuery issued warning when missing(ontologyNames) irrespective-f extact <2012-05-22 Tue>

CHANGES IN VERSION 0.99.8

really using pdfSweave <2012-05-18 Fri>

CHANGES IN VERSION 0.99.7

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>

CHANGES IN VERSION 0.99.6

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>

CHANGES IN VERSION 0.99.5

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>

CHANGES IN VERSION 0.99.4

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>

CHANGES IN VERSION 0.99.3

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>

CHANGES IN VERSION 0.99.2

–lsQuery has a new ‘exact’ parameter <2012-05-04 Fri>

CHANGES IN VERSION 0.99.1

import(XMLSchema) to remove warning at startup <2012-05-04 Fri>

CHANGES IN VERSION 0.99.0

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>

CHANGES IN VERSION 0.2.2

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>

CHANGES IN VERSION 0.2.1

added specific SSOAP and XMLSchema version requirements <2011-12-18 Sun>
fixed a couple-f typos <2011-12-18 Sun>

CHANGES IN VERSION 0.2.0

initial release