Problem getting list of publications for a given TSN

[maurobio]

I have the code below:

library(ritis) # load package
result <- search_scientific(("Vicia faba"))  # search TSN for a scientific name
tsn <- as.integer(result["tsn"]) # get TSN as an integer
pubs <- publications(tsn) # try to get a list of publications for the TSN

But get the error:

Error: $ operator is invalid for atomic vectors

Any hints?

Session Info

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_2.3.2 usethis_2.0.0  ritis_0.9.0   

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        pillar_1.4.7      compiler_4.0.3    plyr_1.8.6        remotes_2.2.0    
 [6] prettyunits_1.1.1 tools_4.0.3       testthat_3.0.1    pkgload_1.1.0     pkgbuild_1.2.0   
[11] jsonlite_1.7.2    memoise_2.0.0     lifecycle_0.2.0   tibble_3.0.5      pkgconfig_2.0.3  
[16] rlang_0.4.10      DBI_1.1.1         cli_2.2.0         rstudioapi_0.13   crul_1.0.0       
[21] curl_4.3          fastmap_1.1.0     withr_2.4.1       dplyr_1.0.3       xml2_1.3.2       
[26] desc_1.2.0        generics_0.1.0    vctrs_0.3.6       fs_1.5.0          rprojroot_2.0.2  
[31] triebeard_0.3.0   tidyselect_1.1.0  glue_1.4.2        httpcode_0.3.0    data.table_1.13.6
[36] R6_2.5.0          processx_3.4.5    fansi_0.4.2       solrium_1.1.4     sessioninfo_1.1.1
[41] callr_3.5.1       purrr_0.3.4       magrittr_2.0.1    ps_1.5.0          urltools_1.7.3   
[46] ellipsis_0.3.1    assertthat_0.2.1  utf8_1.1.4        cachem_1.0.1      crayon_1.3.4     

[sckott]

i can't replicate the issue. try that again and then run traceback() and share that output

[maurobio]

After repeating the sequence of commands:

result <- search_scientific(("Vicia faba"))
tsn <- as.integer(result["tsn"])
pubs <- publications(tsn)

I still get the error message:

Error: $ operator is invalid for atomic vectors

Here are the traceback() results:

6: data.table::rbindlist(x, use.names = TRUE, fill = TRUE)
5: data.table::setDF(data.table::rbindlist(x, use.names = TRUE, 
       fill = TRUE))
4: bindlist(x$referenceFor)
3: dr_op(bindlist(x$referenceFor), "class")
2: cbind(dr_op(x, "referencefor"), dr_op(bindlist(x$referenceFor), 
       "class"))
1: publications(tsn)

[sckott]

sorted back in Sep 2020 i think - see #19 - try again after reinstalling like remotes::install_github("ropensci/ritis")

[maurobio]

I reinstalled the package using devtools::install_github("ropensci/ritis") and it now works fine!

Unfortunately, the version from CRAN is not up-to-date.

Thanks a lot!