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PredictiveEcology / Require

Simple R package to install and load packages conducive to a reproducible workflow
https://require.predictiveecology.org/
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Error: 'getPkgVersions' #96

Closed joburgar closed 1 year ago

joburgar commented 1 year ago

My simInit fails as I get as Require does not seem to have 'getPkgVersions'. I have tried to fix by uninstalling and reinstalling Require and restarting R but these simples steps aren't working. Thoughts?

mySim <- simInit(times = times,

  • params = parameters,
  • modules = modules,
  • objects = list(scenario = data.table(name = "test")),
  • paths = paths) Setting: options( spades.outputPath = 'C:/Users/JBURGAR/R/Analysis/castor/R/scenarios/test_flex2/outputs' spades.modulePath = 'C:/Users/JBURGAR/R/Analysis/castor/R/SpaDES-modules' ) Paths set to: options( rasterTmpDir = 'C:/Users/JBURGAR/AppData/Local/Temp/RtmpoVKiUG/SpaDES/scratch/raster' reproducible.cachePath = 'C:/Users/JBURGAR/AppData/Local/Temp/RtmpoVKiUG/Require/cache' spades.inputPath = 'C:/Users/JBURGAR/AppData/Local/Temp/RtmpoVKiUG/SpaDES/inputs' spades.outputPath = 'C:/Users/JBURGAR/R/Analysis/castor/R/scenarios/test_flex2/outputs' spades.modulePath = 'C:/Users/JBURGAR/R/Analysis/castor/R/SpaDES-modules' spades.scratchPath = 'C:/Users/JBURGAR/AppData/Local/Temp/RtmpoVKiUG/SpaDES/scratch' ) terra::terraOptions(tempdir = 'C:/Users/JBURGAR/AppData/Local/Temp/RtmpoVKiUG/SpaDES/scratch/terra' Error: 'getPkgVersions' is not an exported object from 'namespace:Require'

My session info:

print(sessionInfo()) R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252 [4] LC_NUMERIC=C LC_TIME=English_Canada.1252

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

other attached packages: [1] sqldf_0.4-11 RSQLite_2.2.18 gsubfn_0.7 proto_1.0.0
[5] rgdal_1.5-32 raster_3.6-3 sp_1.5-0 sf_1.0-8
[9] rpostgis_1.4.3 RPostgreSQL_0.7-4 DBI_1.1.3 BalancedSampling_1.6.3 [13] sampling_2.9 RANN_2.6.1 truncnorm_1.0-8 here_1.0.1
[17] forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
[21] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6
[25] tidyverse_1.3.2 keyring_1.3.0 terra_1.6-17 data.table_1.14.4
[29] SpaDES.experiment_0.0.1 SpaDES.core_1.1.0 reproducible_1.2.10 quickPlot_0.1.8

loaded via a namespace (and not attached): [1] googledrive_2.0.0 colorspace_2.0-3 fpCompare_0.2.4 ellipsis_0.3.2
[5] class_7.3-20 rprojroot_2.0.3 Require_0.3.1 fs_1.5.2
[9] fastdigest_0.6-3 rstudioapi_0.14 proxy_0.4-27 listenv_0.9.0
[13] bit64_4.0.5 fansi_1.0.3 lubridate_1.8.0 xml2_1.3.3
[17] codetools_0.2-18 cachem_1.0.6 knitr_1.40 jsonlite_1.8.3
[21] broom_1.0.1 gridBase_0.4-7 dbplyr_2.2.1 rgeos_0.5-9
[25] compiler_4.1.2 httr_1.4.6 backports_1.4.1 assertthat_0.2.1
[29] fastmap_1.1.0 gargle_1.2.1 cli_3.4.1 htmltools_0.5.4
[33] tools_4.1.2 igraph_1.3.5 gtable_0.3.1 glue_1.6.2
[37] fastmatch_1.1-3 Rcpp_1.0.9.5 cellranger_1.1.0 vctrs_0.5.0
[41] DEoptim_2.2-8 xfun_0.34 globals_0.16.2 rvest_1.0.3
[45] lpSolve_5.6.17 lifecycle_1.0.3 googlesheets4_1.0.1 future_1.33.0
[49] MASS_7.3-58.1 scales_1.2.1 hms_1.1.2 parallel_4.1.2
[53] RColorBrewer_1.1-3 qs_0.25.4 yaml_2.3.6 memoise_2.0.1
[57] stringi_1.7.8 e1071_1.7-12 checkmate_2.1.0 boot_1.3-28
[61] chron_2.3-58 rlang_1.0.6 pkgconfig_2.0.3 evaluate_0.17
[65] lattice_0.20-45 bit_4.0.4 tidyselect_1.2.0 parallelly_1.36.0
[69] lobstr_1.1.2 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[73] pillar_1.9.0 haven_2.5.1 whisker_0.4.1 withr_2.5.0
[77] units_0.8-0 future.apply_1.11.0 modelr_0.1.9 crayon_1.5.2
[81] KernSmooth_2.23-20 utf8_1.2.2 RApiSerialize_0.1.2 tzdb_0.3.0
[85] rmarkdown_2.17 grid_4.1.2 readxl_1.4.1 blob_1.2.3
[89] SpaDES.tools_1.0.0 CircStats_0.2-6 reprex_2.0.2 digest_0.6.30
[93] classInt_0.4-8 SamplingBigData_1.0.0 RcppParallel_5.1.5 munsell_0.5.0
[97] stringfish_0.15.7 tcltk_4.1.2

achubaty commented 1 year ago

It looks like you have incompatible versions of Require and SpaDES.core.

You can try downgrading Require (try installing from GitHub using dev-stable branch); or update SpaDES.core along with SpaDES.tools, reproducible, quickPlot, and likely others.

Before making any changes to installed packages, it's worth taking a snapshot of your installed packages (e.g., renv::snapshot() or Require::pkgSnapshot() using the 93-snapshot branch from GitHub).

The development versions of these packages are available via:

pkgs <- "SpaDES.core" # adjust as needed
install.packages(pkgs, repos = c("https://predictiveecology.r-universe.dev/", getOption("repos")))

While these latest versions deal with the transition away from depending on retiring spatial packages in favour of terra and sf, some non-backwards compatible changes were introduced.

joburgar commented 1 year ago

Thanks Alex. That was exactly the issue and loading the development versions worked to fix it.