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ropensci / traits

R package for accessing species trait data from multiple databases
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ncbi_byname('Zea mays','internal transcribed spacer') giving always "Error : Bad Request (HTTP 400)" #125

Closed rodrigo1406 closed 2 years ago

rodrigo1406 commented 3 years ago

My code is simply:

library(traits)
ncbi_byname('Zea mays','internal transcribed spacer')

But it always gives an error message: "Error : Bad Request (HTTP 400)"

What may be going on?

Session Info ```r R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] traits_0.5.0 taxize_0.9.98 loaded via a namespace (and not attached): [1] Rcpp_1.0.5 pillar_1.4.6 compiler_4.0.5 [4] plyr_1.8.6 iterators_1.0.13 tools_4.0.5 [7] digest_0.6.25 uuid_0.1-4 tibble_3.0.4 [10] lifecycle_1.0.0 jsonlite_1.7.1 nlme_3.1-152 [13] lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.10 [16] foreach_1.5.1 cli_2.1.0 rstudioapi_0.11 [19] crul_1.0.0 curl_4.3 parallel_4.0.5 [22] stringr_1.4.0 httr_1.4.2 xml2_1.3.2 [25] rappdirs_0.3.3 vctrs_0.3.4 hms_0.5.3 [28] triebeard_0.3.0 grid_4.0.5 reshape_0.8.8 [31] glue_1.4.2 httpcode_0.3.0 data.table_1.13.0 [34] R6_2.4.1 fansi_0.4.1 conditionz_0.1.0 [37] hoardr_0.5.2 readr_1.4.0 magrittr_1.5 [40] urltools_1.7.3 ellipsis_0.3.1 codetools_0.2-18 [43] rvest_1.0.0 assertthat_0.2.1 bold_1.1.0 [46] ape_5.4-1 stringi_1.5.3 crayon_1.3.4 [49] zoo_1.8-8 ```
sckott commented 3 years ago

thanks for the issue!

please run again, then after the error, run traceback() and paste in the output (BUT MAKE SURE TO EXCLUDE YOUR PRIVATE NCBI API KEY IF YOU SUPPLIED ONE)

rodrigo1406 commented 3 years ago 
> library(traits)
Registered S3 method overwritten by 'hoardr':
  method           from
  print.cache_info httr
> ncbi_byname('Zea mays','internal transcribed spacer')
Working on Zea mays...
...retrieving sequence IDs...
Error : Bad Request (HTTP 400)
NULL
> traceback()
No traceback available 
>
sckott commented 3 years ago

I was able to replicate your issue if I DO NOT have my Entrez API key set. Do you get this in R?

Sys.getenv("ENTREZ_KEY", "")
#> [1] ""

If yes, then you do not have your NCBI Entrez API key set. Try taxize::use_entrez() to get your ENTREZ key, then set your key in R, then try again

maelle commented 2 years ago

This repository is about to be archived.

dlebauer commented 2 years ago

Repository has been unarchived. I've