Closed mkhemmani closed 3 months ago
@mkhemmani As best as I can tell, you are correct: the endpoint has updated. I made a PR (#73) that should fix this, which you can use in the meantime if you'd like.
@mkhemmani This issue appears to have resolved itself - maybe NCBI updated their redirects? unclear.
Looks like both addresses are valid, now.
Hello, I'm having an issue running the taxizedb::name2taxid function on ncbi database taxaonomy
Session Info
─Session info ──────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.3 (2024-02-29 ucrt) os Windows 10 x64 (build 19045) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.utf8 ctype English_United States.utf8 tz America/Chicago date 2024-03-31 rstudio 2023.12.1+402 Ocean Storm (desktop) pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) ─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0) blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0) cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0) cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.3) curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.3) DBI 1.2.2 2024-02-16 [1] CRAN (R 4.3.3) dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.3.3) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.1) digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.3) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.3) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0) evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.3) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.3) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1) generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.3) hoardr 0.5.4 2024-01-23 [1] CRAN (R 4.3.3) htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.3) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.3) httpuv 1.6.14 2024-01-26 [1] CRAN (R 4.3.3) knitr 1.45 2023-10-30 [1] CRAN (R 4.3.3) later 1.3.2 2023-12-06 [1] CRAN (R 4.3.3) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.1) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0) mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0) pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.1) pkgbuild 1.4.3 2023-12-10 [1] CRAN (R 4.3.3) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.3) profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.1) promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.1) purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1) R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0) Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.3) remotes 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.1) rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.3) rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.3.2) RSQLite 2.3.6 2024-03-31 [1] CRAN (R 4.3.3) rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.1) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1) shiny 1.8.0 2023-11-17 [1] CRAN (R 4.3.3) stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.2) stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.3) taxizedb * 0.3.1 2024-04-01 [1] Github (ropensci/taxizedb@3a78dd4) tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.1) tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.3) urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.1) usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.3) utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.3) vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.3) xfun 0.42 2024-02-08 [1] CRAN (R 4.3.3) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0) yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.2) [1] C:/Users/mkhem/AppData/Local/R/win-library/4.3 [2] C:/Program Files/R/R-4.3.3/libraryError in curl::curl_download(db_url, db_path_file, quiet = TRUE) : Could not resolve host: ftp.ncbi.nih.gov
Error in curl::curl_download(db_url, db_path_file, quiet = TRUE) : Could not resolve host: ftp.ncbi.nih.gov
Should the ncbi database url be db_url<-"https://ftp.ncbi.nlm.nih.gov/" ? https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/
NOT ftp.ncbi.nih.gov?