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  o The 'curl' argument to getBM() has been deprecated as it is no longer
  applicable and doesn't do anything.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