NEWS.md
In egonw/BridgeDbR: Code for using BridgeDb identifier mapping framework from within R
BridgeDbR 2.11.2
BUG FIXES
- Fixed build/test process by including a long-running example into the dontrun{} environment
BridgeDbR 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()
BridgeDbR 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)
egonw/BridgeDbR documentation built on Sept. 18, 2023, 8:14 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
BridgeDbR 2.11.2
BUG FIXES
- Fixed build/test process by including a long-running example into the dontrun{} environment
BridgeDbR 2.11.1
NEW FEATURES
- Migrated
NEWStoNEWS.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()
BridgeDbR 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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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