Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ropensci/RNeXML issues and pull requests

#259 - Dependency `XML` requires R>=4.0

Issue - State: open - Opened by hlapp 8 months ago - 2 comments

#258 - `env_unlock()` will be removed from rlang

Issue - State: open - Opened by lionel- 10 months ago - 5 comments

#257 - nexml.org is down, causing tests to fail

Issue - State: closed - Opened by cboettig about 2 years ago - 15 comments

#256 - update CI to v2

Pull Request - State: closed - Opened by cboettig about 2 years ago

#255 - Fixes test failure in prospective dplyr 1.1.x

Pull Request - State: closed - Opened by hlapp about 2 years ago

#254 - Compatibility with dplyr 1.1.0

Issue - State: closed - Opened by lionel- about 2 years ago - 6 comments

#253 - Replaces invocations of dplyr deprecated funcs with supported

Pull Request - State: closed - Opened by hlapp over 2 years ago - 4 comments

#252 - gh-actions check full

Pull Request - State: closed - Opened by cboettig about 3 years ago - 1 comment

#251 - Add RNeXML_ prefix to tree (and other) classes

Issue - State: closed - Opened by krlmlr about 3 years ago - 13 comments

#250 - Warning message: select_() is deprecated as of dplyr 0.7.0

Issue - State: closed - Opened by wdahdul about 4 years ago

#249 - tests fail with new dplyr

Issue - State: closed - Opened by cboettig over 4 years ago - 3 comments

#248 - Fix for dplyr 1.0.0

Pull Request - State: closed - Opened by hadley almost 5 years ago - 1 comment

#247 - Message from CRAN

Issue - State: closed - Opened by cboettig almost 5 years ago - 5 comments

#246 - Explicitly defines column as factor to fix #245

Pull Request - State: closed - Opened by hlapp almost 5 years ago

#245 - breaking change introduced in R 4.0.0

Issue - State: closed - Opened by cboettig almost 5 years ago - 1 comment

#244 - Add official docs url to description

Pull Request - State: closed - Opened by jeroen over 5 years ago - 1 comment

#243 - Ability to drop objects from nexml object

Issue - State: open - Opened by hlapp over 5 years ago

#241 - New release with new summary() etc

Issue - State: closed - Opened by hlapp over 5 years ago - 13 comments
Labels: question

#240 - dplyr methods select_ and mutate_ are deprecated

Issue - State: closed - Opened by hlapp over 5 years ago - 2 comments

#239 - Adding characters fails for some matrices

Issue - State: open - Opened by hlapp over 5 years ago
Labels: bug

#238 - Makes various tests more robust, and uses symbolic address for nexml.org

Pull Request - State: closed - Opened by hlapp over 5 years ago - 1 comment

#237 - Provides a real summary() and improved pretty-print

Pull Request - State: closed - Opened by hlapp over 5 years ago - 2 comments

#236 - Makes character(0) metadata value behave as empty string

Pull Request - State: closed - Opened by hlapp over 5 years ago

#235 - Fixes detection of having to split matrix by class

Pull Request - State: closed - Opened by hlapp over 5 years ago - 5 comments

#234 - Bug in splitting character matrix into continuous and discrete

Issue - State: closed - Opened by hlapp over 5 years ago
Labels: bug

#233 - Print summary doesn't deal properly with zero phylogenetic trees

Issue - State: closed - Opened by hlapp over 5 years ago - 1 comment
Labels: bug

#232 - General purpose accessor functions for nexml object inspection

Issue - State: closed - Opened by hlapp over 5 years ago - 10 comments

#231 - Rmarkdown version of toplevel README no longer necessary?

Issue - State: open - Opened by hlapp almost 6 years ago - 4 comments
Labels: documentation, question

#230 - Thoughts on a hex?

Issue - State: closed - Opened by cboettig about 6 years ago - 3 comments

#229 - Switch over to Additional_repositories for CRAN

Pull Request - State: closed - Opened by cboettig about 6 years ago - 2 comments

#228 - Cut new release to CRAN?

Issue - State: closed - Opened by hlapp about 6 years ago - 5 comments
Labels: question

#227 - Do not add `ter` namespace by default.

Pull Request - State: closed - Opened by cboettig about 6 years ago - 1 comment

#226 - Replace taxize with taxald

Pull Request - State: closed - Opened by cboettig about 6 years ago - 2 comments

#225 - NCBI URIs

Issue - State: closed - Opened by cboettig about 6 years ago - 5 comments

#224 - Replace taxize backend

Issue - State: closed - Opened by cboettig about 6 years ago - 1 comment

#223 - Adds pkgdown site, appveyor, updates readme badges

Pull Request - State: closed - Opened by cboettig about 6 years ago - 6 comments

#222 - Clean up README, or use to build website

Issue - State: closed - Opened by hlapp about 6 years ago - 2 comments

#221 - Adds comparing simplify = FALSE for metadata table

Pull Request - State: closed - Opened by hlapp about 6 years ago - 8 comments

#220 - Fixes how metadata arguments are passed on to add_basic_meta

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#219 - Fixes CDAO namespace definition

Pull Request - State: closed - Opened by hlapp about 6 years ago - 2 comments

#218 - Enables handling of files with rootedge

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#217 - Fixes levels "trees" and "characters" being ignored in add_meta()

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#216 - Refactors extraction of metadata by property

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#215 - Adds a utility function for expanding prefixed strings

Pull Request - State: closed - Opened by hlapp about 6 years ago - 2 comments

#214 - Reconfigures codecov success thresholds

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#213 - add_meta() doesn't work for level "trees" and "characters"

Issue - State: closed - Opened by hlapp about 6 years ago
Labels: bug

#212 - Reconfigures manuscript on CircleCI to run only on master

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#211 - Reconfigure (or disable) manuscript rebuilds on Circle CI

Issue - State: closed - Opened by hlapp about 6 years ago - 2 comments

#210 - Fixes NAs in containing element IDs for nested meta

Pull Request - State: closed - Opened by hlapp about 6 years ago - 5 comments

#209 - Fixes a couple small typos

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#208 - Adds constructors for all classes in the hierarchy

Pull Request - State: closed - Opened by hlapp about 6 years ago - 2 comments

#207 - rootEdge disposable?

Issue - State: closed - Opened by hlapp about 6 years ago - 3 comments
Labels: question

#206 - Silences warnings about undeclared/unknown classes in method defs

Pull Request - State: closed - Opened by hlapp about 6 years ago - 1 comment

#205 - Fixes duplicate S4 class name issues without changing class names

Pull Request - State: closed - Opened by hlapp about 6 years ago - 5 comments

#204 - Ensure NULL list elements in nexml slots are not converted to XML

Pull Request - State: closed - Opened by hlapp about 6 years ago - 2 comments

#203 - Refactors the S4 class structure for meta elements

Pull Request - State: closed - Opened by hlapp over 6 years ago - 3 comments

#202 - Fixes several bugs in handling metadata

Pull Request - State: closed - Opened by hlapp over 6 years ago - 2 comments

#201 - Makes most S4 classes in the package pseudo-namespaced

Pull Request - State: closed - Opened by hlapp over 6 years ago - 4 comments

#200 - Enables parsing and serialization of XML-type literal metas

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#199 - Adds simplify option for table returned by get_metadata()

Pull Request - State: closed - Opened by hlapp over 6 years ago - 8 comments

#198 - Includes nested meta elements in get_metadata() result

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#197 - Fix blank node behavior of nested meta elements

Pull Request - State: closed - Opened by cboettig over 6 years ago - 2 comments

#196 - Failure to handle nested meta elements

Issue - State: closed - Opened by hlapp over 6 years ago - 5 comments
Labels: bug

#195 - Adds description of changes for next release

Pull Request - State: closed - Opened by hlapp over 6 years ago

#194 - Regenerates man pages with markdown support turned on

Pull Request - State: closed - Opened by hlapp over 6 years ago

#193 - Patch LiteralMeta use of literal node text

Pull Request - State: closed - Opened by cboettig over 6 years ago

#192 - Fix serialization of polymorphic and uncertain states

Pull Request - State: closed - Opened by cboettig over 6 years ago

#191 - Polymorphic (and probably uncertain) states fail to get written out in write.nexml()

Issue - State: closed - Opened by hlapp over 6 years ago - 3 comments
Labels: bug

#190 - Certain metadata is getting lost upon reading NeXML

Issue - State: closed - Opened by hlapp over 6 years ago - 3 comments
Labels: bug

#189 - patch circle ci

Pull Request - State: closed - Opened by cboettig over 6 years ago - 1 comment

#188 - Fixes type coercion for morphological characters with polymorphic states

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#187 - Provide API to query for member states of polymorphic and uncertain states

Issue - State: open - Opened by hlapp over 6 years ago
Labels: use-case

#185 - Plans for update release to CRAN?

Issue - State: closed - Opened by hlapp over 6 years ago - 10 comments
Labels: question

#184 - Drops unneeded suggested dependency on phylobase

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#183 - Various test failures with devtools::test()

Issue - State: closed - Opened by hlapp over 6 years ago - 1 comment
Labels: bug, question

#182 - Housekeeping for build and check artifacts to be ignored

Pull Request - State: closed - Opened by hlapp over 6 years ago

#181 - Makes test suite more robust, including to missing packages

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#180 - .Rd files under version control

Issue - State: closed - Opened by hlapp over 6 years ago - 2 comments
Labels: question

#179 - Dependencies for package check recursively bring in this package

Issue - State: closed - Opened by hlapp over 6 years ago - 2 comments

#178 - test_publish.R is skipped silently in its entirety

Issue - State: open - Opened by hlapp over 6 years ago - 3 comments

#177 - taxize_nexml tests are inconsistently in part run and in part skipped on CRAN

Issue - State: closed - Opened by hlapp over 6 years ago - 5 comments

#176 - taxize_nexml() fails to call use_entrez()

Issue - State: closed - Opened by hlapp over 6 years ago - 1 comment
Labels: bug

#175 - Provide API to query for polymorphic and uncertain states

Issue - State: closed - Opened by hlapp over 6 years ago
Labels: use-case

#174 - Fixes broken handling of polymorphic and uncertain states

Pull Request - State: closed - Opened by hlapp over 6 years ago - 1 comment

#173 - Patch polymorphic / uncertain state type

Pull Request - State: closed - Opened by cboettig over 6 years ago - 5 comments

#172 - Handling of polymorphic and uncertain character states is badly broken

Issue - State: closed - Opened by hlapp over 6 years ago - 10 comments
Labels: bug

#169 - clash with "tree" class name provided by cli package

Issue - State: closed - Opened by fmichonneau over 6 years ago - 6 comments
Labels: bug

#165 - phyloXML: Separate R package or not?

Issue - State: closed - Opened by gvegayon about 7 years ago - 8 comments

#161 - xml matrix with polymorphic states

Issue - State: closed - Opened by laurajackson almost 8 years ago - 7 comments

#153 - Updated rendering of README markdown file

Pull Request - State: closed - Opened by hlapp over 8 years ago - 1 comment

#140 - Packages uses IDs instead of labels when labels are non-unique

Issue - State: closed - Opened by hlapp about 9 years ago - 2 comments

#90 - Other options for `nexml_publish()`

Issue - State: closed - Opened by sckott over 10 years ago - 11 comments
Labels: question

#87 - add coercion methods to/from phylobase formats

Issue - State: closed - Opened by cboettig over 10 years ago - 1 comment

#75 - add_meta should error if abbreviation is not defined in namespaces

Issue - State: open - Opened by cboettig over 10 years ago - 1 comment
Labels: bug

#67 - taxonomy - handling alternative authority sources other than NCBI

Issue - State: closed - Opened by sckott almost 11 years ago

#66 - taxonomy - taxize tool user interface (interactive prompts)

Issue - State: closed - Opened by sckott almost 11 years ago - 1 comment

#55 - phyloxml support?

Issue - State: closed - Opened by cboettig almost 11 years ago - 13 comments
Labels: question