kguidonimartins
commented
2 years ago Hi @oliveirab! Thanks for reporting this issue. Please, could you provide the results of sessionInfo()?
Closed oliveirab closed 1 year ago
kguidonimartins
commented
2 years ago Hi @oliveirab! Thanks for reporting this issue. Please, could you provide the results of sessionInfo()?
oliveirab
commented
2 years ago Yep!
sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages:
[1] parallel grid stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] bdc_1.1.1 ggrepel_0.9.1 rcol_0.2.0 taxadb_0.1.5
[5] taxizedb_0.3.0 taxize_0.9.100 rinat_0.1.8 rvertnet_0.8.2
[9] pbapply_1.5-0 traitdataform_0.6.8 writexl_1.4.0 googledrive_2.0.0
[13] readxl_1.4.0 forcats_0.5.1 stringr_1.4.0 purrr_0.3.4
[17] readr_2.1.2 tidyr_1.2.0 tibble_3.1.7 tidyverse_1.3.1
[21] ggvenn_0.1.9 ggplot2_3.3.6 DT_0.22 dplyr_1.0.9
[25] knitr_1.39 data.table_1.14.2
loaded via a namespace (and not attached):
[1] uuid_1.1-0 backports_1.4.1 plyr_1.8.7
[4] lazyeval_0.2.2 sp_1.4-7 crosstalk_1.2.0
[7] RApiSerialize_0.1.0 digest_0.6.29 foreach_1.5.2
[10] htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3
[13] memoise_2.0.1 tzdb_0.3.0 modelr_0.1.8
[16] RcppParallel_5.1.5 duckdb_0.3.4 askpass_1.1
[19] prettyunits_1.1.1 colorspace_2.0-3 blob_1.2.3
[22] rvest_1.0.2 rappdirs_0.3.3 hoardr_0.5.2.93
[25] haven_2.5.0 xfun_0.30 rgdal_1.5-31
[28] crayon_1.5.1 RCurl_1.98-1.6 jsonlite_1.8.0
[31] stringfish_0.15.7 zoo_1.8-10 iterators_1.0.14
[34] ape_5.6-2 glue_1.6.2 gtable_0.3.0
[37] gargle_1.2.0 maps_3.4.0 arkdb_0.0.15
[40] scales_1.2.0 oai_0.3.2 contentid_0.0.15
[43] DBI_1.1.2 miniUI_0.1.1.1 Rcpp_1.0.8.3
[46] xtable_1.8-4 progress_1.2.2 units_0.8-0
[49] proxy_0.4-26 bit_4.0.4 bold_1.2.0
[52] rgbif_3.7.2 htmlwidgets_1.5.4 httr_1.4.3
[55] geosphere_1.5-14 ellipsis_0.3.2 farver_2.1.0
[58] pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.9
[61] sass_0.4.1 dbplyr_2.1.1 utf8_1.2.2
[64] here_1.0.1 conditionz_0.1.0 crul_1.2.0
[67] labeling_0.4.2 tidyselect_1.1.2 rlang_1.0.2
[70] reshape2_1.4.4 later_1.3.0 munsell_0.5.0
[73] cellranger_1.1.0 tools_4.2.1 cachem_1.0.6
[76] cli_3.3.0 generics_0.1.2 RSQLite_2.2.14
[79] broom_0.8.0 evaluate_0.15 fastmap_1.1.0
[82] sys_3.4 yaml_2.3.5 bit64_4.0.5
[85] fs_1.5.2 nlme_3.1-157 whisker_0.4
[88] mime_0.12 xml2_1.3.3 compiler_4.2.1
[91] rstudioapi_0.13 curl_4.3.2 e1071_1.7-9
[94] reprex_2.0.1 bslib_0.3.1 stringi_1.7.6
[97] rgeos_0.5-9 rgnparser_0.2.0 lattice_0.20-45
[100] classInt_0.4-3 vctrs_0.4.1 pillar_1.7.0
[103] lifecycle_1.0.1 jquerylib_0.1.4 bitops_1.0-7
[106] raster_3.5-15 httpuv_1.6.5 R6_2.5.1
[109] qs_0.25.3 promises_1.2.0.1 KernSmooth_2.23-20
[112] codetools_0.2-18 assertthat_0.2.1 openssl_2.0.0
[115] CoordinateCleaner_2.0-20 rprojroot_2.0.3 withr_2.5.0
[118] rcrossref_1.1.0 httpcode_0.3.0 rnaturalearth_0.1.0
[121] hms_1.1.1 terra_1.5-21 class_7.3-20
[124] suppdata_1.1-8 rmarkdown_2.14 sf_1.0-7
[127] getPass_0.2-2 shiny_1.7.1 lubridate_1.8.0 I guess this could be an error from {rgnparser}. Please, try the
standalone installation of gnparser and run bdc::bdc_clean_names()
again. Follow the steps below:
## install/load `rgnparser`
if (!require("rgnparser")) install.packages("rgnparser")
## install the gnparser binary
rgnparser::install_gnparser()
## run `bdc::bdc_clean_names()` again with your species list.I doesn't seem to be working...
if (!require("rgnparser")) install.packages("rgnparser")
Loading required package: rgnparser
Attaching package: ‘rgnparser’
The following object is masked from ‘package:taxize’:
gn_parse
rgnparser::install_gnparser()
The latest gnparser version is v1.6.5
Error in utils::download.file(grep(os, urls, value = TRUE), file, mode = "wb") :
lengths of 'url' and 'destfile' must match
bdc::bdc_clean_names(splist$species_original[1:100])
The latest gnparser version is v1.6.5
Error in utils::download.file(grep(os, urls, value = TRUE), file, mode = "wb") :
lengths of 'url' and 'destfile' must matchThanks again, @oliveirab! Pretty sure this is a rgnparser problem. We can try a few tests if you want. The first one is to reinstall the rgnparser from our fork. I made little changes to prevent errors you are reporting, like:
Error in utils::download.file(grep(os, urls, value = TRUE), file, mode = "wb") : lengths of 'url' and 'destfile' must match
Reload your R session (close and reopen the RStudio for example) before trying the following steps:
## reinstall `rgnparser`
if (!require("remotes")) install.packages("remotes")
remotes::install_github("bdc-proj/rgnparser", force = TRUE)
## install the gnparser binary
rgnparser::install_gnparser()
## rerun your consult using `bdc`
bdc::bdc_clean_names(splist$species_original[1:100])
hazeljanderson
commented
1 year ago @oliveirab this is an old issue so not sure if you have moved on or found a workaround by now.
This seems to be a common issue and I found
this article helpful which suggests using wininet
options(download.file.method = "wininet")
kguidonimartins
commented
1 year ago Thanks, @hazeljanderson! Maybe that option could solve the problem. As you note, this is an old issue without any activity in the last few months. I'm proposing to close this issue for now. But feel free to open it again when needed.
Hi folks, I've been trying to use bdc_clean_names and I am getting the following error message:
I appreciate any guidance.