BUG FIXES
BUG FIXES
secondary vignetteNEW FEATURES
sec2pri identifier mappings databases can be usedBUG FIXES
BUG FIXES
NEW FEATURES
NEWS to NEWS.mdexists(mapper, xref) that checks if the xref is found in the mapping fileSIGNIFICANT USER-VISIBLE CHANGES
loadDatabase() now reports an error if the given location does not existBUG FIXES
getMatchingSources()map()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)