Changes in version 2.11.2 BUG FIXES - Fixed build/test process by including a long-running example into the dontrun{} environment Changes in version 2.11.1 NEW FEATURES - Migrated NEWS to NEWS.md - Applied BioC code styling - Added templates for issues and feature requests - Added a method exists(mapper, xref) that checks if the xref is found in the mapping file SIGNIFICANT USER-VISIBLE CHANGES - loadDatabase() now reports an error if the given location does not exist BUG FIXES - Fixed backwards compatibility of map() - Clarified in the vignette the output getMatchingSources() - Fixed returning an empty data frame when no mappings are found for map() Changes in version 2.9.2 - Updated to BridgeDb 3.0.21 Older versions: CHANGES IN VERSION 2.9.1 ------------------------ NEW FEATURES o Updated to BridgeDb 3.0.19 CHANGES IN VERSION 2.7.5 ------------------------ BUG FIXES o Fixed a method definition CHANGES IN VERSION 2.7.4 ------------------------ NEW FEATURES o improved code CHANGES IN VERSION 2.7.3 ------------------------ NEW FEATURES o Updated to BridgeDb 3.0.14 o Support primary/secondary identifier annotation o Added mapping Bioregistry.io compact identifiers o Added getting a DataSource by their Bioregistry.io prefix BUG FIXES o Fixed some metadata in the package Rmd CHANGES IN VERSION 2.5.0 ------------------------ NEW FEATURES o Updated to BridgeDb 3.0.13 BUG FIXES o Small typo fix in a code example in the Vignette CHANGES IN VERSION 2.1.2 ------------------------- BUG FIXES o Fixed the link to the webpage to download mapping files CHANGES IN VERSION 1.99.1 ------------------------- BUG FIXES o no more downloading of databases in the examples CHANGES IN VERSION 1.99.0 ------------------------- BUG FIXES o Added missing NEWS section for 1.23.1 o BridgeDb 3.0.0-SNAPSHOT (2020-10-18) CHANGES IN VERSION 1.23.1 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o no longer supports 32bit on Windows CHANGES IN VERSION 1.21.6 ------------------------- NEW FEATURES o adds a getProperties() method o adds a maps() method that can map multiple identifiers SIGNIFICANT USER-LEVEL CHANGES o the map() method now returns a data frame CHANGES IN VERSION 1.21.5 ------------------------- BUG FIXES o fixed links in the Vignette and some further clarification CHANGES IN VERSION 1.21.4 ------------------------- BUG FIXES o updated the Apache Derby library to 10.5.3.0 (fixing compatibility with newer ID mapping databases) NEW FEATURES o Updated to BridgeDb 2.3.0 o replaced RCurl with curl to fix downloading on Windows CHANGES IN VERSION 1.21.3 ------------------------- BUG FIXES o force RCurl to use TSL1.2 o added clarification of external data sources used CHANGES IN VERSION 1.21.2 ------------------------- BUG FIXES o updated URL of the /data/gene_database/ location to point directly to bridgedb.github.io o now uses the smaller Bs mapping database as test data in the example o updated the code for getDatabase() to allow downloading data from any location provided by /data/gene_database/ CHANGES IN VERSION 1.21.1 ------------------------- BUG FIXES o no longer tries to get Derby file names online CHANGES IN VERSION 1.17.5 ------------------------- NEW FEATURES o added a link to the vignette to the Figshare Metabolics ID mapping database collection CHANGES IN VERSION 1.17.4 ------------------------- BUG FIXES o added missing link to the Bioconductor webpage in the vignette CHANGES IN VERSION 1.17.3 ------------------------- NEW FEATURES o added an attempt to have BioSchemas annotation in the vignette o now points to the issue tracker of the new GitHub code repository CHANGES IN VERSION 1.17.2 ------------------------- NEW FEATURES o added getAttributes() that returns the attributes (properties) for the given identifier CHANGES IN VERSION 1.17.1 ------------------------- NEW FEATURES o server location for getDatabase() can now be configured with the website parameter BUG FIXES o Fixed the default database download server URL (now uses https) CHANGES IN VERSION 1.15.1 ------------------------- NEW FEATURES o README now uses BiocManager for instructions how to install the package CHANGES IN VERSION 1.15.1 ------------------------- NEW FEATURES o Updated to BridgeDb 2.3.0 CHANGES IN VERSION 1.13.6 ------------------------- NEW FEATURES o Uses BibTeX again (in the RMarkdown tutorial) o Added a section on metabolomics to the tutorial CHANGES IN VERSION 1.13.5 ------------------------- NEW FEATURES o Added to the Metabolomics and Cheminformatics views CHANGES IN VERSION 1.13.4 ------------------------- NEW FEATURES o Converted the vignette to RMarkdown CHANGES IN VERSION 1.13.3 ------------------------- BUG FIXES o Fixed the URLs for GitHub and the issue tracker CHANGES IN VERSION 1.13.2 ------------------------- NEW FEATURES o Restored the original README.md for visitors of GitHub particularly CHANGES IN VERSION 1.13.1 ------------------------- NEW FEATURES o Added information on how to manually download mapping databases CHANGES IN VERSION 1.11.5 ------------------------- NEW FEATURES o Added ORCID id for a few authors/maintainers CHANGES IN VERSION 1.11.4 ------------------------- BUG FIXES o Updated to BridgeDb 2.2.2: fixes recognition of new HMDB identifiers (closes #1) CHANGES IN VERSION 1.10.2 ------------------------- BUG FIXES o Fixed the NEWS for 1.10.1 CHANGES IN VERSION 1.10.1 ------------------------- NEW FEATURES o More unit tests BUG FIXES o Updated to BridgeDb 2.2.0: fixes loading of mapping files with new data sources CHANGES IN VERSION 1.9.3 ------------------------ NEW FEATURES o adds a method to register a new DataSource o adds methods to see if a DataSource exists, based on the full name and system code BUG FIXES o Updated file pattern for getBridgeNames() CHANGES IN VERSION 1.7.2 ------------------------ NEW FEATURES o Now has a test suite SIGNIFICANT USER-LEVEL CHANGES o Depends on R 3.3 BUG FIXES o Bug fixes introduced in versions 1.3.2 and 1.3.3 CHANGES IN VERSION 1.3.3 ------------------------ BUG FIXED o fixed returning of GO mappings (Lars Eijssen) CHANGES IN VERSION 1.3.2 ------------------------ BUG FIXED o fixed the getting for BridgeDb database names for recent download server updates o added better documentation for loadDatabase() CHANGES IN VERSION 1.3.1 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Depend on R 3.2 CHANGES IN VERSION 1.3.0 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o getOrganismCode() now throws an error when the given species was not found o map() can now also return all possible mappings o getBridgeNames() now also supports other locations and custom file name patterns NEW FEATURES o adds unit testing (with testthat) o updated vignette for new user-visible changes o updated the BridgeDb libraries to version 2.1.0 BUG FIXES o added license infromation for Java libraries (Apache Derby and BridgeDb) o fixed a wrong descriptiong in the documentation of loadDatabse() o download of BridgeDb identifier mappings files is now forces as binary fixing the downloading on MS-Windows platforms o source code line length according to Bioconductor CHANGES IN VERSION 0.99.1 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o No changes NEW FEATURES o New package BUG FIXES o No changes classified as 'bug fixes' (package under active development)