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snp without class fails with ncbi_snp_query() #163

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jooolia opened this issue Jan 13, 2023 · 1 comment
Closed

snp without class fails with ncbi_snp_query() #163

jooolia opened this issue Jan 13, 2023 · 1 comment
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@jooolia
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jooolia commented Jan 13, 2023

Please do not submit bug reports for issues with the OpenSNP or NCBI’s dbSNP server itself. rsnps is only an API client, it does not have control over the server hosting the data.

Describe the bug
A clear and concise description of what the bug is.

Code to reproduce
ncbi_snp_query("rs539690682")

Expected behaviour
Should give NCBI information about snp. Instead gives error:

Error in if (Class %in% c("snv", "snp", "delins")) { :
argument is of length zero

OS and R versions (please complete the following information):

  • OS: [e.g., Windows10, macOS, Linux] macOS
  • R Version [e.g., 3.6.2] 4.1.1

Session Info: devtools::session_info() or sessionInfo()

Session Info
Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.1 (2021-08-10)
 os       macOS Catalina 10.15.7
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2023-01-13
 rstudio  2022.02.3+492 Prairie Trillium (desktop)
 pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package     * version    date (UTC) lib source
   brio          1.1.3      2021-11-30 [1] CRAN (R 4.1.0)
   cachem        1.0.6      2021-08-19 [1] CRAN (R 4.1.0)
   callr         3.7.2      2022-08-22 [1] CRAN (R 4.1.2)
   cli           3.5.0      2022-12-20 [1] CRAN (R 4.1.1)
   crayon        1.5.1      2022-03-26 [1] CRAN (R 4.1.2)
   crul          1.3        2022-09-03 [1] CRAN (R 4.1.2)
   curl          4.3.3      2022-10-06 [1] CRAN (R 4.1.2)
   data.table    1.14.6     2022-11-16 [1] CRAN (R 4.1.2)
   desc          1.4.2      2022-09-08 [1] CRAN (R 4.1.2)
   devtools      2.4.4      2022-07-20 [1] CRAN (R 4.1.2)
   digest        0.6.29     2021-12-01 [1] CRAN (R 4.1.0)
   ellipsis      0.3.2      2021-04-29 [1] CRAN (R 4.1.0)
   evaluate      0.16       2022-08-09 [1] CRAN (R 4.1.2)
   fansi         1.0.3      2022-03-24 [1] CRAN (R 4.1.2)
   fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.1.0)
   fs            1.5.2      2021-12-08 [1] CRAN (R 4.1.0)
   glue          1.6.2      2022-02-24 [1] CRAN (R 4.1.2)
   htmltools     0.5.3      2022-07-18 [1] CRAN (R 4.1.2)
   htmlwidgets   1.5.4      2021-09-08 [1] CRAN (R 4.1.0)
   httpcode      0.3.0      2020-04-10 [1] CRAN (R 4.1.0)
   httpuv        1.6.6      2022-09-08 [1] CRAN (R 4.1.2)
   httr          1.4.4      2022-08-17 [1] CRAN (R 4.1.2)
   jsonlite      1.8.4      2022-12-06 [1] CRAN (R 4.1.2)
   knitr         1.40       2022-08-24 [1] CRAN (R 4.1.2)
   later         1.3.0      2021-08-18 [1] CRAN (R 4.1.0)
   lifecycle     1.0.3      2022-10-07 [1] CRAN (R 4.1.2)
   magrittr      2.0.3      2022-03-30 [1] CRAN (R 4.1.2)
   memoise       2.0.1      2021-11-26 [1] CRAN (R 4.1.0)
   mime          0.12       2021-09-28 [1] CRAN (R 4.1.0)
   miniUI        0.1.1.1    2018-05-18 [1] CRAN (R 4.1.0)
   pillar        1.8.1      2022-08-19 [1] CRAN (R 4.1.2)
   pkgbuild      1.3.1      2021-12-20 [1] CRAN (R 4.1.0)
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 4.1.0)
   pkgload       1.3.0      2022-06-27 [1] CRAN (R 4.1.2)
   plyr          1.8.8      2022-11-11 [1] CRAN (R 4.1.2)
   prettyunits   1.1.1      2020-01-24 [1] CRAN (R 4.1.0)
   processx      3.7.0      2022-07-07 [1] CRAN (R 4.1.2)
   profvis       0.3.7      2020-11-02 [1] CRAN (R 4.1.0)
   promises      1.2.0.1    2021-02-11 [1] CRAN (R 4.1.0)
   ps            1.7.1      2022-06-18 [1] CRAN (R 4.1.2)
   purrr         0.3.4      2020-04-17 [1] CRAN (R 4.1.0)
   R6            2.5.1      2021-08-19 [1] CRAN (R 4.1.0)
   Rcpp          1.0.9      2022-07-08 [1] CRAN (R 4.1.2)
   remotes       2.4.2      2021-11-30 [1] CRAN (R 4.1.0)
   rlang         1.0.6      2022-09-24 [1] CRAN (R 4.1.2)
   rmarkdown     2.16       2022-08-24 [1] CRAN (R 4.1.2)
   rprojroot     2.0.3      2022-04-02 [1] CRAN (R 4.1.2)
 P rsnps       * 0.5.0.9000 2023-01-13 [?] load_all()
   rstudioapi    0.14       2022-08-22 [1] CRAN (R 4.1.2)
   sessioninfo   1.2.2      2021-12-06 [1] CRAN (R 4.1.0)
   shiny         1.7.2      2022-07-19 [1] CRAN (R 4.1.2)
   stringi       1.7.8      2022-07-11 [1] CRAN (R 4.1.1)
   stringr       1.5.0      2022-12-02 [1] CRAN (R 4.1.2)
   testthat    * 3.1.4      2022-04-26 [1] CRAN (R 4.1.1)
   tibble        3.1.8      2022-07-22 [1] CRAN (R 4.1.2)
   triebeard     0.3.0      2016-08-04 [1] CRAN (R 4.1.0)
   urlchecker    1.0.1      2021-11-30 [1] CRAN (R 4.1.0)
   urltools      1.7.3      2019-04-14 [1] CRAN (R 4.1.0)
   usethis       2.1.6      2022-05-25 [1] CRAN (R 4.1.2)
   utf8          1.2.2      2021-07-24 [1] CRAN (R 4.1.0)
   vctrs         0.5.1      2022-11-16 [1] CRAN (R 4.1.2)
   withr         2.5.0      2022-03-03 [1] CRAN (R 4.1.2)
   xfun          0.33       2022-09-12 [1] CRAN (R 4.1.2)
   xtable        1.8-4      2019-04-21 [1] CRAN (R 4.1.0)
   yaml          2.3.5      2022-02-21 [1] CRAN (R 4.1.2)

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@jooolia
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jooolia commented Mar 3, 2023

fixed in #164.

@jooolia jooolia closed this as completed Mar 3, 2023
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