ropensci/taxizedb issues and pull requests

#85 - Increase test coverage

Issue - State: open - Opened by stitam 6 months ago

#84 - New database - ICTV

Issue - State: open - Opened by stitam 6 months ago

#83 - Prepare COL locally

Issue - State: closed - Opened by stitam 6 months ago

#82 - Prepare TPL locally

Issue - State: closed - Opened by stitam 6 months ago

#81 - Prepare all SQLite databases locally

Pull Request - State: closed - Opened by stitam 6 months ago - 1 comment

#80 - `worms`, `bold` dbs listed in `children` db but are unsupported (`run_with_db`)

Issue - State: closed - Opened by KaiAragaki 6 months ago - 2 comments

#79 - tracking lineage on wikidata db

Issue - State: closed - Opened by mdrishti 6 months ago - 4 comments

#78 - `taxize` and `taxizedb` return different `tibble` structures with `children` when `db = "itis"`

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

#77 - Prepare GBIF SQLite database locally

Issue - State: closed - Opened by stitam 8 months ago

#76 - Repeat of #63

Issue - State: closed - Opened by KaiAragaki 8 months ago - 4 comments

#75 - Children test failing (pt 2)

Issue - State: closed - Opened by KaiAragaki 8 months ago - 1 comment

#74 - Could not resolve host: ftp.ncbi.nih.gov

Issue - State: closed - Opened by mkhemmani 8 months ago - 3 comments

#73 - update ncbi endpoint

Pull Request - State: closed - Opened by KaiAragaki 8 months ago - 2 comments

#72 - Allow the use of a custom datafiles in db_load_* functions

Pull Request - State: open - Opened by arendsee 10 months ago - 1 comment

#71 - change db and cache path

Issue - State: open - Opened by bergalu about 1 year ago - 2 comments

#70 - missing species names for name2taxid

Issue - State: closed - Opened by hh1985 about 1 year ago - 4 comments

#69 - 404 error with db_download_gbif()

Issue - State: closed - Opened by pederengelstad over 1 year ago - 3 comments

#68 - How to unify the list generated after classification?

Issue - State: open - Opened by lauraDRH over 1 year ago - 8 comments
Labels: feature

#67 - Update README and CITATION

Pull Request - State: closed - Opened by stitam over 1 year ago

#66 - Update to standard R-check workflow

Pull Request - State: closed - Opened by stitam over 1 year ago

#65 - Final edits before releasing v0.3.1

Pull Request - State: closed - Opened by stitam over 1 year ago

#64 - How to get ta taxonomy table from taxizedb?

Issue - State: open - Opened by GossypiumH over 1 year ago - 2 comments

#63 - GBIF database empty

Issue - State: closed - Opened by NgAMB almost 2 years ago - 3 comments
Labels: bug

#62 - Release taxizedb 0.3.1

Issue - State: closed - Opened by stitam almost 2 years ago - 1 comment

#61 - remove email address for scott from DESCRIPTION

Pull Request - State: closed - Opened by sckott almost 2 years ago

#60 - Restore readme.md

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

#59 - Can't download ITIS db

Issue - State: closed - Opened by juanmayorgahenao over 2 years ago - 4 comments

#58 - add option for curl override

Pull Request - State: closed - Opened by kylebuscaglia over 2 years ago

#57 - Query works with taxize but doesn't work with taxizedb

Issue - State: open - Opened by stitam about 3 years ago - 5 comments

#56 - Transform ropensci.github.io in docs.ropensci.org

Pull Request - State: closed - Opened by Rekyt over 3 years ago - 1 comment

#55 - names2taxid issue with catalogue of life

Issue - State: open - Opened by aguilart over 3 years ago - 10 comments

#54 - Possible bug: using 'downstream' function with World Flora Online

Issue - State: closed - Opened by kwymangrothem almost 4 years ago - 3 comments
Labels: bug

#53 - Downstream intermediates argument?

Issue - State: closed - Opened by sagesteppe about 4 years ago - 3 comments

#52 - Using taxize and taxizedb

Issue - State: closed - Opened by brunobrr about 4 years ago - 15 comments

#51 - Is there a `parents` function?

Issue - State: closed - Opened by Midnighter about 4 years ago - 10 comments
Labels: feature

#50 - failing tests on cran

Issue - State: closed - Opened by sckott about 4 years ago - 1 comment

#49 - Add World Flora Online as a data source

Issue - State: closed - Opened by sckott over 4 years ago

#48 - fixes for ITIS downstream/classification/children

Issue - State: closed - Opened by sckott over 4 years ago

#47 - Data Source: World Flora Online

Issue - State: closed - Opened by aravind-j almost 5 years ago - 2 comments
Labels: data-source

#46 - 404 error when downloading COL

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

#45 - children test failing

Issue - State: open - Opened by sckott almost 6 years ago - 3 comments

#44 - downstream possible bug

Issue - State: closed - Opened by sckott almost 6 years ago - 11 comments

#43 - db_load_itis() fails after successful install with "psql not found on your computer"

Issue - State: closed - Opened by twest820 over 6 years ago - 10 comments

#42 - fix bug in 'name2taxid' for organism names with underscores originally

Pull Request - State: closed - Opened by gpli over 6 years ago - 7 comments

#41 - "name2taxid" can't handle names with underscores correctly

Issue - State: closed - Opened by gpli over 6 years ago - 4 comments

#40 - Wikidata data source

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

#39 - EOL data source

Issue - State: closed - Opened by sckott over 6 years ago - 14 comments
Labels: data-source

#38 - change to mariadb in pkg, only affects COL right now

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

#37 - wikidata data source

Issue - State: closed - Opened by sckott over 6 years ago - 1 comment

#36 - move away from RMySQL

Issue - State: closed - Opened by andzandz11 over 6 years ago - 4 comments

#35 - Add optional progress to download functions

Issue - State: closed - Opened by sckott over 6 years ago

#34 - Add parameter to download functions to optionally update

Issue - State: closed - Opened by sckott over 6 years ago - 7 comments

#33 - Patch circle-ci

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

#32 - possibly use cached `taxize` objects for test suite?

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

#31 - `db_download`: add parameter to force re-download of the DB

Issue - State: closed - Opened by sckott over 6 years ago - 1 comment

#30 - database tests and debugging

Pull Request - State: closed - Opened by cboettig over 6 years ago - 11 comments

#29 - load_gbif incorrectly claims 'sqlite3 not available'

Issue - State: closed - Opened by cboettig over 6 years ago - 7 comments

#28 - db_load_* functions don't take host address

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

#27 - `name2taxid` includes some questionable material

Issue - State: open - Opened by arendsee over 6 years ago - 4 comments

#26 - update gbif sqlite data

Issue - State: closed - Opened by sckott over 6 years ago - 1 comment

#25 - Extend new NCBI functionality to the other databases

Issue - State: closed - Opened by arendsee almost 7 years ago - 2 comments

#24 - Protect against SQL injection attacks

Issue - State: closed - Opened by sckott almost 7 years ago - 5 comments

#23 - Unnest hierarchy table and add `taxid2rank` and `downstream` functions

Pull Request - State: closed - Opened by arendsee almost 7 years ago - 14 comments

#22 - Fix #21

Pull Request - State: closed - Opened by arendsee almost 7 years ago - 2 comments

#21 - taxizedb::name2taxid fails on duplicated names

Issue - State: closed - Opened by arendsee almost 7 years ago - 1 comment

#20 - Add `children`, `taxid2name`, `name2taxid` and `name2taxid_map` functions

Pull Request - State: closed - Opened by arendsee almost 7 years ago - 10 comments

#19 - Add `classification` function

Pull Request - State: closed - Opened by arendsee about 7 years ago - 12 comments

#18 - Import NCBI taxonomy table as SQLite DB

Pull Request - State: closed - Opened by arendsee about 7 years ago - 14 comments

#17 - Add a vignette

Issue - State: closed - Opened by sckott about 7 years ago - 3 comments

#16 - with dplyr update, need dbplyr

Issue - State: closed - Opened by sckott over 7 years ago

#15 - man page on troubleshooting installation of SQL libraries

Issue - State: closed - Opened by sckott over 7 years ago - 1 comment

#14 - improve docs on auth details for each database type

Issue - State: closed - Opened by sckott over 7 years ago - 1 comment

#13 - Fix example code for Catalogue of Life database download

Pull Request - State: closed - Opened by tdjames1 over 7 years ago - 4 comments

#12 - maybe remove backend_set/_get for now?

Issue - State: closed - Opened by sckott over 7 years ago

#11 - add checks for whether SQL dbs running/on

Issue - State: closed - Opened by sckott over 7 years ago

#10 - use sys instead of system()

Issue - State: closed - Opened by sckott over 7 years ago - 2 comments

#9 - Use hoardr for caching

Issue - State: closed - Opened by sckott over 7 years ago

#8 - Use gbif-backbone-sql on S3 for GBIF backbone source

Issue - State: closed - Opened by sckott over 7 years ago

#7 - downstream sql version in inst/ignore

Issue - State: closed - Opened by sckott almost 8 years ago

#6 - downloading error in `db_download_*` functions (due to missing directory .taxize_local)

Issue - State: closed - Opened by dlebauer over 8 years ago - 5 comments
Labels: bug

#5 - possibly have sqlite as an option

Issue - State: closed - Opened by sckott over 8 years ago - 1 comment

#4 - Feedback

Issue - State: closed - Opened by sckott over 8 years ago - 7 comments

GitHub / ropensci/taxizedb issues and pull requests