rentrez (development version)
BUG FIXES
entrez_link()now reports what NCBI said when a reply carries no usable content. A command NCBI will not serve comes back as HTTP 200 with an<ERROR>inside the LinkSet, and five of the ninecmdparsers ran on into a subscript or a names error that named no cause (#215).entrez_link(cmd = "llinks")and its siblings return an empty set for an ID that has no linkouts, where they used to fail. An ID with nothing to link is an answer rather than a failure, so only a reply carrying an NCBI error stops now.entrez_search()reports what NCBI said when a search comes back with no result, rather than failing on a subscript. NCBI answers a bad database name with an ordinary HTTP 200 whose body carries the reason, and the JSON path did not check for it at all, soretmode = "json"returned a record built from missing pieces that then failed when printed (#187).Requests that send more than 200 IDs now use POST, as intended. The check that chooses POST over GET ran after the IDs had been collapsed into a single string, so it never matched and every request used GET (#174, thanks @allenbaron).
MINOR IMPROVEMENTS
HTTP failures name the query that caused them, with the API key removed. The key reaches these messages two ways, in the query string whenever one is set and quoted back by NCBI when it rejects one, and these messages get pasted into bug reports (#159).
Removed stray characters from two error messages (#211).
rentrez 1.2.4
CRAN release: 2025-06-11
Maintenance release to meet CRAN policies.
- S3 methods are now registered with
@exportS3Methodinstead of being exported directly. - Documentation links to the XML package are now fully qualified.
rentrez 1.2.3
CRAN release: 2020-11-10
Maintenance release, mostly to prevent issues with rate-limiting errors when the package is tested in CRAN.
The sleep commands for rate-limiting are slightly increased
As of this release, the vignette is NOT build by default (to avoid issues with automated tests on CRAN). This will not affect most users, but a developers may want to read a wiki page describing how to build the vignette:
https://github.com/ropensci/rentrez/wiki/Building-the-rentrez-tutorial-vignette.
rentrez 1.2.2
CRAN release: 2019-05-02
Maintenance release containing a number of bug fixes.
- A fix #127 forces curl to use http/1.1, as NCBI produces errors when sing http/2 (thanks @hammer for bug report and fix)
- fix #131 stops pubmed records with reference sections production > 1 value for the ‘pmid’ field. Thanks @agbarnett for the report.
- Added clarification around the expectd input for
extract_from_esummaryto the docs.
rentrez 1.2.1
CRAN release: 2018-03-05
Bug fix release. Thanks @gmbecker for pointing out a problem with the way retmode was being used in entrez_fetch (PR #121).
Also updates documentation to make this clear. Removes depricated verbs from testthat code.
rentrez 1.2.0
CRAN release: 2018-02-11
rentrez updated to reflect NCBIs new API policy, allowing more requests from users with registered keys. (Issues #115 – #117).
CITATION updated to reflect publication in The R Journal.
Minor changes * clarification of search syntax in docs (issue #120) * ORCID ids added for all authors (issue #118)
rentrez 1.1.0
CRAN release: 2017-06-01
As of this release, rentrez will use httr::POST when sending > 200 ids to the NCBI. This should make working with large ID sets easier (thanks to the NCBI for supporing the POST methods, Reed Cartwright and Chris Stubben for pushing me on issue #89).
Other minor changes: * Pass on error messages from NCBI when too many records are requested from entrez_summary (Issue #106) * Useful error message when trying to send an empty ID set to NCBI (Issue #107)
rentrez 1.0.4
CRAN release: 2016-10-26
Update to documentation and tests to accommodate versioned accessions now available from NCBI (see ?entrez_fetch and the vignette)
rentrez 1.0.3
Update to only use https * NCBI is goinh all https, rentrez will only use https from now on. * Added links to repo/bug reporting to DESCRIPTION * Documented changes to sequence database XML records * Allow automatic parsing of XML flavours
rentrez 1.0.2
CRAN release: 2016-04-21
Bug fix release * Tests now work with testthat 1.0.0 * All calls to ncbi specify encoding is UTF-8 (saving error messages) * HTTP Error codes associated with large requests now give the user a hint to check out the documentation for web-history features
rentrez 1.0.1
CRAN release: 2016-02-29
Bug fix release * Properly format “by_id” mode URLS (bug exposed by httr 1.0.1) * Handle case in which some IDs passed to “by_id” mode are invalide (thanks Zachary Foster for report) * Documentation updated to reflect OMIM->SNP links no longer possible * Use Rmarkdown (not knitr) as vignette builder * Return NCBI error messages are text when they exist
rentrez 1.0.0
CRAN release: 2015-09-23
* new function extract_from_esummary() for extracting like-named elements
from a list esummary records (e.g. get all "Title" fields from a list of
PubMed esummaries)
* Support for `cmd` option in entrez_link (breaks backward compatibility)
* Allows discovery of external links from and use of web_history
* New helper function linkout_urls to get URLs form external links
* Support for 'by_id' mode for entrez_link. Pass a vector of IDs to
entrez_link, (optionally) get a list on elink objects back (one per ID)
* New web_history object makes using NCBI Web History features easier
* All of these changes documented in new vignette
* Han Guangchun added as contributor for his pull requests
* New tests, minor bug fixes and extended documentationrentrez 0.4.1
CRAN release: 2015-03-03
- Bug fix: The example for entrez_summary contained a typo which made it fail (being wrapped in dontest this hadn’t previously shown up).
rentrez 0.4
CRAN release: 2015-02-09
- entrez_summary now fetches ‘version 2.0’ esummary records from NCBI
- This change may break some scripts. In particular, the names of some elements in esummary records have changed. Broken scripts shold produce a helpful error message, and using entrez_summary(…, version=“1.0”) should fix it. More details are given in the help to entrez_summary.
- When version 2.0 records are requested entrez_summary fetches the json record.
- New helper functions for einfo Eutil
- entrez_dbs() lists avaliable databases.
- entrez_db_summary() gets summary information about a given database.
- entrez_db_links() lists databases against which a given db’s records might be cross referenced.
- entrez_db_searchable() lists search terms avaliable for a given database.
- Nicer print functions for search and summary objects
- New dependancy on jsonlite for handling json records.
- Bunch of bugs squashed and typos cleaned up