Changelog

Source: NEWS.md

rols 2.99

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  • REST queries now use httr2 instead of superseded httr.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

rols 2.29

CHANGES IN VERSION 2.29.1

  • Fix unit tests.

CHANGES IN VERSION 2.29.0

  • New devel version (Bioc 3.18)

rols 2.25

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)

rols 2.24

CHANGES IN VERSION 2.24.0

  • New release version (Bioc 3.15)

rols 2.23

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

rols 2.21

CHANGES IN VERSION 2.21.1

  • Fix failing unit test

CHANGES IN VERSION 2.21.0

  • New devel version for Bioc 3.14

rols 2.19

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)

rols 2.17

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)

rols 2.16

CHANGES IN VERSION 2.16.0

  • Bioconductor release version (Bioc 3.11)

rols 2.15

CHANGES IN VERSION 2.15.0

  • Bioconductor version bump

rols 2.13

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>

rols 2.11

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)

rols 2.10

CHANGES IN VERSION 2.10.0

  • New version for Bioc 3.8 (release)

rols 2.9

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

CHANGES IN VERSION 2.9.0

  • Bioconductor devel

rols 2.8

CHANGES IN VERSION 2.8.0

  • Bioconductor release

rols 2.7

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

rols 2.6

CHANGES IN VERSION 2.6.0

  • Bioconductor release 3.6

rols 2.5

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

rols 2.4

CHANGES IN VERSION 2.4.0

  • Bioconductor release 3.5

rols 2.3

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 <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

rols 2.2

CHANGES IN VERSION 2.2.0

  • Bioconductor release 3.4

CHANGES IN VERSION 2.1.3

  • Fix failing tests <2016-09-16 Fri>

rols 1.99

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

rols 1.13

CHANGES IN VERSION 1.13.1

  • Package deprecation message <2015-12-30 Wed>

CHANGES IN VERSION 1.13.0

  • Bioc devel 3.3

rols 1.12

CHANGES IN VERSION 1.12.0

  • Bio release 3.2

rols 1.11

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>

rols 1.10

CHANGES IN VERSION 1.11.0

  • Bioc devel 3.2

CHANGES IN VERSION 1.10.0

  • Bioc release 3.1

rols 1.7

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

rols 1.6

CHANGES IN VERSION 1.6.0

  • release for Bioc 2.14

rols 1.5

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

rols 1.3

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

rols 1.2

CHANGES IN VERSION 1.2.0

  • Bioc 2.12 stable version bump

rols 1.1

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>

rols 0.99

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>

rols 0.2

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