版本变化2.58.0 - - - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o getSequence()将提供更多信息的错误消息,如果请求旁侧序列,而不是提供一个上游或下游范围。o删除引用中国镜子,现在已经退休(https://www.ensembl.info/2023/01/13/retirement-of-ensembl-us-west-aws-mirror/)的变化版本2.56.0 - - - - - - - - - - - - - - - - - - - - - - - - - o修复BUG修复问题当多个缓存条目可以创建相同的ID。(由于Herve页& Henrik Bengtsson独立这个问题的报告。)o bmRequest()现在将尊重设置选项(“超时”)的变化版本2.52.0 - - - - - - - - - - - - - - - - - - - - - - - - - BUG修复o停止报告信息的使用https使用useEnsembl时(),一个“版本”的论点。o使用virtualSchemaName提供的集市,而不是简单的“默认”。这使得问题运用植物集市。2.50.0版本的变化- - - - - - - - - - - - - - - - - - - - - - - - -小变化o useMart()和listMarts()将提醒用户如果使用http访问运用。从2021年底https将实施运用。BUG修复o地址问题检查列表运用档案会阻止所有查询工作如果主要的www.ensembl.org网站不可用。o修复bug引入getSequence()要求侧翼序列导致无效的查询。o参数“主机”不再是忽略useEnsembl()(感谢论坛用户“A”(https://support.bioconductor.org/p/9139019/)的变化版本2.48.0 - - - - - - - - - - - - - - - - - - - - - - - - - o getSequence新特性()现在允许关闭缓存通过“useCache”的论点。 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.