Example in map new concepts not working
Closed this issue · 4 comments
The new_source() function throws an error when executing the following example block.
# already existing ontology for some project about crops
crops <- load_ontology(path = system.file("extdata", "crops.rds", package = "ontologics"))
# where we have to set the external dataset as new source
crops <- new_source(name = "externalDataset",
description = "a vocabulary",
homepage = "https://www.something.net",
license = "CC-BY-4.0",
ontology = crops)
# new concepts that occur in the external dataset, which should be harmonised with the ontology
newConcepts <- c("Wheat", "NUTS", "Avocado")I think this is caused by giving only 5 arguments to the function, where it actually has 6 arguments. The default value for the 6th argument (notes) is NULL, as we see in the function's head:
new_source <- function(name = NULL, description = NULL, homepage = NULL, license = NULL, notes = NULL, ontology = NULL)Apparently, this leads to a conflict with the sources Data.Frame that expects to get a chr-type object for the notes column (at least that is what I get from the error :D). Here is the error stack:
Error: Internal error in `vec_proxy_assign_opts()`: `proxy` of type `character` incompatible with `value` proxy of type `NULL`.
Traceback:
1. new_source(name = "externalDataset", description = "a vocabulary",
. homepage = "https://www.something.net", license = "CC-BY-4.0",
. ontology = crops)
2. bind_rows(ontology@sources, newSource) # at line 68 of file C:/Users/arner/Nextcloud/Projects/ontologics/R/new_source.R
3. vec_rbind(!!!dots, .names_to = .id)
4. (function ()
. abort(message = message))()
5. abort(message = message)
6. signal_abort(cnd)
Strange. This shouldn't be happening. Maybe it's due to some other package not having the correct version. I don't get this error msg and also the github actions don't pick it up.
Could you please run sessionInfo()? Mine shows
> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C LC_TIME=German_Germany.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ontologics_0.3.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 magrittr_2.0.3 hms_1.1.1 tidyselect_1.1.2 R6_2.5.1 rlang_1.0.2 fansi_1.0.3 stringr_1.4.0 dplyr_1.0.9
[10] tools_4.2.0 checkmate_2.1.0 utf8_1.2.2 cli_3.3.0 DBI_1.1.2 ellipsis_0.3.2 assertthat_0.2.1 tibble_3.1.7 lifecycle_1.0.1
[19] crayon_1.5.1 tidyr_1.2.0 purrr_0.3.4 readr_2.1.2 tzdb_0.3.0 vctrs_0.4.1 glue_1.6.2 stringi_1.7.6 compiler_4.2.0
[28] pillar_1.7.0 generics_0.1.2 backports_1.4.1 pkgconfig_2.0.3
I might then have to declare clearer the import-section of the package...
Hm. Then it is probably related to my environment. I run the code in a jupyter notebook from the top level folder and load the ontologics package with devtools. Let's investigate this when the restructuring of the package's internals is finished. For now, I append the sessionInfo (I'll try updating R today) and the contents of the notebook:
SessionInfo():
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ontologics_0.3.1 tibble_2.1.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 pillar_1.4.2 compiler_3.6.1 remotes_2.4.0
[5] prettyunits_1.0.2 base64enc_0.1-3 tools_3.6.1 testthat_3.0.3
[9] pkgload_1.2.1 pkgbuild_1.2.0 zeallot_0.1.0 digest_0.6.21
[13] uuid_0.1-2 lifecycle_1.0.0 jsonlite_1.6 evaluate_0.14
[17] memoise_2.0.0 checkmate_1.9.4 pkgconfig_2.0.2 rlang_0.4.11
[21] rstudioapi_0.13 IRdisplay_0.7.0 cli_2.5.0 IRkernel_1.2
[25] fastmap_1.1.0 withr_2.4.2 repr_1.1.3 dplyr_0.8.3
[29] stringr_1.4.0 desc_1.3.0 vctrs_0.2.0 fs_1.5.0
[33] hms_0.5.0 devtools_2.4.2 rprojroot_1.3-2 tidyselect_0.2.5
[37] glue_1.3.1 R6_2.5.0 processx_3.5.2 sessioninfo_1.1.1
[41] pbdZMQ_0.3-3 callr_3.7.0 purrr_0.3.4 readr_1.3.1
[45] tidyr_0.8.3 magrittr_2.0.1 usethis_2.0.1 ps_1.6.0
[49] backports_1.1.4 htmltools_0.3.6 ellipsis_0.3.2 assertthat_0.2.1
[53] stringi_1.4.3 cachem_1.0.5 crayon_1.3.4
notebook:
devtools::load_all()
library(tibble)
# already existing ontology for some project about crops
crops <- load_ontology(path = system.file("extdata", "crops.rds", package = "ontologics"))
# where we have to set the external dataset as new source
crops <- new_source(name = "externalDataset",
description = "a vocabulary",
homepage = "https://www.something.net",
license = "CC-BY-4.0",
ontology = crops)
# new concepts that occur in the external dataset, which should be harmonised with the ontology
newConcepts <- c("Wheat", "NUTS", "Avocado")Hm, I think you should, first of all, update your R installation, the current version is 4.2, and I think with that come many new updates, for instance in the tidyverse...
Yeah, it apparently was a version issue.