CHANGES IN biomaRt VERSION 2.66.0
USER VISIBLE CHANGES
- This package documentation is now available as a pkgdown website at https://huber-group-embl.github.io/biomaRt/.
BUG FIXES
getGene()no longer errors with “This function only works when used with the ensembl BioMart.”, that was always returned, even when using the ensembl BioMart. This bug was introduced in version 2.27.1 (Bioconductor 3.3). Thanks to Tobias Hoch for the report.This package now explicitly depends on R >= 4.1.0. This was effectively already the case since version 2.58, in line with Bioconductor policy, but not explicitly documented in
DESCRIPTION.
INTERNAL CHANGES
Coding style throughout the package has been harmonized using the air tool. Contributors using RStudio, Positron or VS Code should have their code styled automatically on save.
A duplicated definition of the
.getEnsemblSSL()internal function has been removed.Static analysis via the lintr package is now performed on each push and PR. It should mostly be invisible to users but might result in slightly increased performance in some cases.
This package now uses roxygen2 to generate documentation and
NAMESPACE.A
R CMD checkNOTEabout a missing import has been resolved.This package continuous integration setup now errors on
R CMD checkWARNINGs. This is checked on each push and PR.The digest and rappdirs dependencies have been removed in favour of functions provided by the base R tools package.
CHANGES IN biomaRt VERSION 2.62.0
BUG FIXES
Results returned from BioMart queries will be read using Latin-1 encounding if the default fails. Reported in https://support.bioconductor.org/p/9158844/ (Backported to 2.60.1)
Fixed issue when only one dataset was listed in a Mart instance, causing data.frame dimensions to be dropped. This broke connectivity to https://parasite.wormbase.org. (Backported to 2.60.1)
CHANGES IN biomaRt VERSION 2.60.0
USER VISIBLE CHANGES
listEnsemblGenomes() and useEnsemblGenomes() now have a host argument, allowing you to select an Ensembl Genomes archive site. (Thanks to Hervé Pagès @hpages for the suggestion: https://github.com/grimbough/biomaRt/issues/93)
The ‘curl’ argument to getBM() has been deprecated as it is no longer applicable and doesn’t do anything.
CHANGES IN biomaRt VERSION 2.58.0
USER VISIBLE CHANGES
getSequence() will now provide a more informative error message if requesting a flanking sequence and not provided with an upstream or downstream range.
Remove references to the uswest mirror, which has now been retired (https://www.ensembl.info/2023/01/13/retirement-of-ensembl-us-west-aws-mirror/)
CHANGES IN biomaRt VERSION 2.50.0
MINOR CHANGES
- useMart() and listMarts() will warn users if using http to access Ensembl. https will be enforced by Ensembl from late 2021.
BUG FIXES
Address issue where checking the list of Ensembl Archives would stop all queries from working if the main www.ensembl.org site was unavailable.
Fix bug introduced in getSequence() where asking for flanking sequences resulted in an invalid query.
The argument ‘host’ is no longer ignored in useEnsembl() (Thanks to forum user “A” - https://support.bioconductor.org/p/9139019/)
CHANGES IN biomaRt VERSION 2.48.0
NEW FEATURES
getSequence() now allows the cache to be turned off via the ‘useCache’ argument.
Automatic detection of SSL issues with Ensembl, and appropriate settings applied to httr functions used by biomaRt.
BUG FIXES
Addressed issue with getSequence() and ID types that are not available on the ‘sequences’ page. This could result in truncated sequences being returned from a query.
getBM() would fail if it found a cache entry, but the file was corrupted. Invalid entries are now detected and deleted if encountered.
CHANGES IN biomaRt VERSION 2.42.0
NEW FEATURES
- The results of queries will now be cached, and if repeated queries are detected the results are loaded from disk.
CHANGES IN biomaRt VERSION 2.36.0
BUG FIXES
Patched problem returning the list of available datasets, if the description of one or more datasets included an apostrophe (introduced with new primate species in Ensembl).
Caught scenario where ensemblRedirect=FALSE was still being ignored.
Changed query submission when redirection is detected to cope with apparently new behaviour of the Ensembl mirrors.
CHANGES IN biomaRt VERSION 2.34.0
NEW FEATURES
- Added the listEnsemblArchives() function. This returns a table of the available Ensembl archives, and replaces the archive = TRUE argument to several functions, which was no longer working.
BUG FIXES
- The Ensembl BioMart server doesn’t always respond well if queries with more than 500 filter values are submitted. If a query that exceed this is detect biomaRt will now submit the query in batches and concatonate the result when completed.
MINOR CHANGES
- You can now provide a host with ‘http://’ at the start, or a trailing ‘/’ (typically copy/pasted from a browser) and useMarts() etc will cope.