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o The 'curl' argument to getBM() has been deprecated as it is no longer
applicable and doesn't do anything.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