CHANGES IN VERSION 2.66.0 ------------------------- INTERNAL CHANGES o 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. CHANGES IN VERSION 2.64.0 ------------------------- BUG FIXES o Version 1.10 of {httr2} changed how URLs are parsed, and this broke some biomaRt functionality. This has been patched. (Backported to biomaRt 2.62.1) CHANGES IN VERSION 2.62.0 ------------------------- USER VISIBLE CHANGES o Several deprecated functions are now defunct. BUG FIXES o 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) o 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 VERSION 2.60.0 ------------------------- USER VISIBLE CHANGES o 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https://github.com/grimbough/biomaRt/issues/93) o The 'curl' argument to getBM() has been deprecated as it is no longer applicable and doesn't do anything. INTERNAL CHANGES o Removed dependency on XML package and switched all functionality to xml2 o Swiched from httr to httr2 package for submitting queries to BioMart servers. CHANGES IN VERSION 2.58.0 ------------------------- USER VISIBLE CHANGES o getSequence() will now provide a more informative error message if requesting a flanking sequence and not provided with an upstream or downstream range. o 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 VERSION 2.56.0 ------------------------- BUG FIXES o 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.) o bmRequest() will now respect the setting in options("timeout") CHANGES IN VERSION 2.52.0 ------------------------- BUG FIXES o Stop reporting message about the use of https when using useEnsembl() with a 'version' argument. o Use virtualSchemaName provided by a Mart, rather than simply "default". This caused issues with the Ensembl Plants Mart. CHANGES IN VERSION 2.50.0 ------------------------- MINOR CHANGES o useMart() and listMarts() will warn users if using http to access Ensembl. https will be enforced by Ensembl from late 2021. BUG FIXES o Address issue where checking the list of Ensembl Archives would stop all queries from working if the main www.ensembl.org site was unavailable. o Fix bug introduced in getSequence() where asking for flanking sequences resulted in an invalid query. o The argument 'host' is no longer ignored in useEnsembl() (Thanks to forum user "A" - https://support.bioconductor.org/p/9139019/) CHANGES IN VERSION 2.48.0 ------------------------- NEW FEATURES o getSequence() now allows the cache to be turned off via the 'useCache' argument. o Automatic detection of SSL issues with Ensembl, and appropriate settings applied to httr functions used by biomaRt. BUG FIXES o 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. o 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 VERSION 2.46.0 ------------------------- BUG FIXES o getLDS() now detects if trying to use datasets from different Marts and reports this to the user. CHANGES IN VERSION 2.42.0 ------------------------- NEW FEATURES o The results of queries will now be cached, and if repeated queries are detected the results are loaded from disk. MINOR CHANGES o 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. o Unused argument 'ssl.verifypeer' removed from listMarts() and useMarts(). o RCurl removed from package dependecies. BUG FIXES o Improvements made to selecting the correct port when using http vs https o Results that contain unescaped new line characters are now returned successfully. CHANGES IN VERSION 2.36.0 ------------------------- BUG FIXES o 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). o Caught scenario where ensemblRedirect=FALSE was still being ignored. o Changed query submission when redirection is detected to cope with apparently new behaviour of the Ensembl mirrors. MINOR CHANGES o Increase query timeout limit to 5 minutes. CHANGES IN VERSION 2.34.0 ------------------------- NEW FEATURES o 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 o 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 o 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. CHANGES IN VERSION 2.32.0 ------------------------- BUG FIXES o Fixed bug when columns were not returned in the order requested, which resulted in the wrong column names being added to the result. CHANGES IN VERSION 2.30.0 ------------------------- SIGNIFICANT USER-LEVEL CHANGES o Updated vignette to use BiocStyle and execute most code chunks.