NEWS

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biomaRt 2.62.0

USER VISIBLE CHANGES

• Several deprecated functions are now defunct.

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)

biomaRt 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• The 'curl' argument to getBM() has been deprecated as it is no longer applicable and doesn't do anything.

INTERNAL CHANGES

• Removed dependency on XML package and switched all functionality to xml2
• Swiched from httr to httr2 package for submitting queries to BioMart servers.

biomaRt 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/)

biomaRt 2.56.0

BUG FIXES

• Fix problem when multiple cache entries with the same ID could be created. (Thanks to Hervé Pagès & Henrik Bengtsson for independent reports of this issue.)
• bmRequest() will now respect the setting in options("timeout")

biomaRt 2.52.0

BUG FIXES

• Stop reporting message about the use of https when using useEnsembl() with a 'version' argument.
• Use virtualSchemaName provided by a Mart, rather than simply "default". This caused issues with the Ensembl Plants Mart.

biomaRt 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/)

biomaRt 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.

biomaRt 2.46.0

BUG FIXES

• getLDS() now detects if trying to use datasets from different Marts and reports this to the user.

biomaRt 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.

MINOR CHANGES

• Ensembl users will be redirected to their closest mirror unless the host argument is explicitly provided. In this case the defined value will be enforced.
• Unused argument 'ssl.verifypeer' removed from listMarts() and useMarts().
• RCurl removed from package dependecies.

BUG FIXES

• Improvements made to selecting the correct port when using http vs https
• Results that contain unescaped new line characters are now returned successfully.

biomaRt 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.

MINOR CHANGES

• Increase query timeout limit to 5 minutes.

biomaRt 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.

biomaRt 2.32.0

BUG FIXES

• Fixed bug when columns were not returned in the order requested, which resulted in the wrong column names being added to the result.

biomaRt 2.30.0

SIGNIFICANT USER-LEVEL CHANGES

• Updated vignette to use BiocStyle and execute most code chunks.