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) 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.