Closed amoeba closed 3 years ago
Yup, you must have upgraded duckdb
and new versions aren't yet backwards compatible. The easiest thing is to purge taxadb_dir()
,
unlink(taxadb:::taxadb_dir())
we should probably provide a helper function since that isn't even an exported fn. Hopefully duckdb will hit 1.0 soon and this will be less of an issue!
Ah, okay. Nuking taxadb:::taxadb_dir()
got things back to working. Thanks!
While running
EML::set_taxonomicCoverage
withexpand=TRUE
, I ran into an error which can be reproduced fromtaxadb
directly:I did a bit of looking and it seems like there's some infrastructure I don't entirely understand that generates a database dump that might just need to get re-run? Any ideas @cboettig?
``` > devtools::session_info() ─ Session info ─────────────────────────────────────────────────────────────── setting value version R version 4.1.0 (2021-05-18) os macOS Big Sur 10.16 system x86_64, darwin17.0 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Juneau date 2021-06-02 ─ Packages ─────────────────────────────────────────────────────────────────── package * version date lib source arkdb 0.0.12 2021-04-05 [1] CRAN (R 4.1.0) askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0) blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) cachem 1.0.5 2021-05-15 [1] CRAN (R 4.1.0) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0) cli 2.5.0 2021-04-26 [1] CRAN (R 4.1.0) contentid 0.0.10 2021-04-27 [1] CRAN (R 4.1.0) crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0) curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0) DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0) dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.0) desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.0) devtools 2.4.1 2021-05-05 [1] CRAN (R 4.1.0) digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0) dplyr 1.0.6 2021-05-05 [1] CRAN (R 4.1.0) duckdb 0.2.6 2021-05-09 [1] CRAN (R 4.1.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) EML * 2.0.5 2021-02-27 [1] CRAN (R 4.1.0) emld 0.5.1 2020-09-27 [1] CRAN (R 4.1.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0) generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0) glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0) hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.0) htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0) jqr 1.2.1 2021-05-06 [1] CRAN (R 4.1.0) jsonld 2.2 2020-05-27 [1] CRAN (R 4.1.0) jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0) knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0) openssl 1.4.4 2021-04-30 [1] CRAN (R 4.1.0) pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0) pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.1.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0) progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) R6 2.5.0 2020-10-28 [1] CRAN (R 4.1.0) rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.1.0) Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.1.0) readr 1.4.0 2020-10-05 [1] CRAN (R 4.1.0) remotes 2.4.0 2021-06-02 [1] CRAN (R 4.1.0) rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0) rmarkdown 2.8 2021-05-07 [1] CRAN (R 4.1.0) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0) RSQLite 2.2.7 2021-04-22 [1] CRAN (R 4.1.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0) taxadb * 0.1.3 2021-04-27 [1] CRAN (R 4.1.0) testthat 3.0.2 2021-02-14 [1] CRAN (R 4.1.0) tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0) tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0) usethis 2.0.1 2021-02-10 [1] CRAN (R 4.1.0) utf8 1.2.1 2021-03-12 [1] CRAN (R 4.1.0) uuid 0.1-4 2020-02-26 [1] CRAN (R 4.1.0) V8 3.4.2 2021-05-01 [1] CRAN (R 4.1.0) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0) withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0) xfun 0.23 2021-05-15 [1] CRAN (R 4.1.0) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library ```session_info() output