CRAN Package Check Results for Maintainer ‘Sven Verweij <sven.verweij at nmi-agro.nl>’

Last updated on 2025-12-28 03:52:18 CET.

Package	ERROR	NOTE	OK
OBIC	1	3	9

Package OBIC

Current CRAN status: ERROR: 1, NOTE: 3, OK: 9

Version: 4.0.0
Check: examples
Result: ERROR Running examples in 'OBIC-Ex.R' failed The error most likely occurred in: > ### Name: calc_grass_age > ### Title: Calculate the average age of the grass > ### Aliases: calc_grass_age > > ### ** Examples > > calc_grass_age(ID = rep(1,5), B_LU_BRP = c(1091,265,256,256,1091)) Error in `[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, : attempt access index 5/5 in VECTOR_ELT Calls: calc_grass_age -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 4.0.0
Check: tests
Result: ERROR Running 'testthat.R' [9s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library(testthat) > library(OBIC) > > setDTthreads(1) > test_check("OBIC") Saving _problems/test-crop_rotation-10.R Saving _problems/test-grass_age-9.R Saving _problems/test-nematode-118.R Saving _problems/test-nematode-156.R Saving _problems/test-nematode-187.R Saving _problems/test-obic_farm-4.R Saving _problems/test-obic_field_dt-115.R Saving _problems/test-obic_field_dt-144.R Saving _problems/test-recommendations-6.R [ FAIL 9 | WARN 0 | SKIP 0 | PASS 160 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-crop_rotation.R:2:3'): calc_grass_age works ──────────────────── Error in ``[.data.table`(dt, , `:=`(this_frc, sum(sel)/.N), by = ID)`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-crop_rotation.R:2:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::calc_rotation_fraction(...) 5. ├─dt[, `:=`(this_frc, sum(sel)/.N), by = ID] 6. └─data.table:::`[.data.table`(...) ── Error ('test-grass_age.R:2:3'): calc_grass_age works ──────────────────────── Error in ``[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-grass_age.R:2:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::calc_grass_age(...) 5. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 6. └─data.table:::`[.data.table`(...) ── Error ('test-nematode.R:93:3'): ind_nematodes works with complete input ───── Error in ``[.data.table`(dt.melt, , `:=`(value, evaluate_logistic(x = number, b = nem_b, x0 = nem_x, v = nem_v, increasing = FALSE)), by = c("element"))`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-nematode.R:93:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::ind_nematodes(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ── Error ('test-nematode.R:131:3'): ind_nematodes works with complete input but with missing values ── Error in ``[.data.table`(dt.melt, , `:=`(value, evaluate_logistic(x = number, b = nem_b, x0 = nem_x, v = nem_v, increasing = FALSE)), by = c("element"))`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-nematode.R:131:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::ind_nematodes(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ── Error ('test-nematode.R:162:3'): ind_nematodes works with incomplete input ── Error in ``[.data.table`(dt.melt, , `:=`(value, evaluate_logistic(x = number, b = nem_b, x0 = nem_x, v = nem_v, increasing = FALSE)), by = c("element"))`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-nematode.R:162:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::ind_nematodes(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ── Error ('test-obic_farm.R:4:1'): (code run outside of `test_that()`) ───────── Error in ``[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─OBIC::obic_farm(dt) at test-obic_farm.R:4:1 2. └─OBIC::obic_field_dt(dt = dt, output = c("scores", "indicators")) 3. └─OBIC::obic_field(...) 4. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))] 5. └─data.table:::`[.data.table`(...) 6. └─base::eval(jsub, SDenv, parent.frame()) 7. └─base::eval(jsub, SDenv, parent.frame()) 8. └─OBIC::calc_grass_age(ID, B_LU_BRP) 9. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 10. └─data.table:::`[.data.table`(...) ── Error ('test-obic_field_dt.R:61:3'): obic_field_dt works ──────────────────── Error in ``[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-obic_field_dt.R:61:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::obic_field_dt(tdt) 5. └─OBIC::obic_field(...) 6. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))] 7. └─data.table:::`[.data.table`(...) 8. └─base::eval(jsub, SDenv, parent.frame()) 9. └─base::eval(jsub, SDenv, parent.frame()) 10. └─OBIC::calc_grass_age(ID, B_LU_BRP) 11. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 12. └─data.table:::`[.data.table`(...) ── Error ('test-obic_field_dt.R:130:3'): obic_field_dt() works with just required columns ── Error in ``[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_equal(...) at test-obic_field_dt.R:130:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─OBIC::obic_field_dt(stdt, output = "scores") 5. └─OBIC::obic_field(...) 6. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))] 7. └─data.table:::`[.data.table`(...) 8. └─base::eval(jsub, SDenv, parent.frame()) 9. └─base::eval(jsub, SDenv, parent.frame()) 10. └─OBIC::calc_grass_age(ID, B_LU_BRP) 11. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 12. └─data.table:::`[.data.table`(...) ── Error ('test-recommendations.R:6:1'): (code run outside of `test_that()`) ─── Error in ``[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass))`: attempt access index 5/5 in VECTOR_ELT Backtrace: ▆ 1. └─OBIC::obic_farm(dt) at test-recommendations.R:6:1 2. └─OBIC::obic_field_dt(dt = dt, output = c("scores", "indicators")) 3. └─OBIC::obic_field(...) 4. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))] 5. └─data.table:::`[.data.table`(...) 6. └─base::eval(jsub, SDenv, parent.frame()) 7. └─base::eval(jsub, SDenv, parent.frame()) 8. └─OBIC::calc_grass_age(ID, B_LU_BRP) 9. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 10. └─data.table:::`[.data.table`(...) [ FAIL 9 | WARN 0 | SKIP 0 | PASS 160 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 4.0.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'description-of-the-columns.Rmd' using rmarkdown --- finished re-building 'description-of-the-columns.Rmd' --- re-building 'obic_introduction.Rmd' using rmarkdown Quitting from obic_introduction.Rmd:119-144 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace: ▆ 1. └─OBIC::obic_field(...) 2. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))] 3. └─data.table:::`[.data.table`(...) 4. └─base::eval(jsub, SDenv, parent.frame()) 5. └─base::eval(jsub, SDenv, parent.frame()) 6. └─OBIC::calc_grass_age(ID, B_LU_BRP) 7. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)] 8. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'obic_introduction.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building 'obic_introduction.Rmd' --- re-building 'obic_score_aggregation.Rmd' using rmarkdown Quitting from obic_score_aggregation.Rmd:390-390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ attempt access index 5/5 in VECTOR_ELT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from obic_score_aggregation.Rmd:390-390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ `[.data.table`(dt, , `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, , grass)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'obic_score_aggregation.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building 'obic_score_aggregation.Rmd' --- re-building 'obic_water_functions.Rmd' using rmarkdown --- finished re-building 'obic_water_functions.Rmd' --- re-building 'obic_workability.Rmd' using rmarkdown Quitting from obic_workability.Rmd:61-82 [plot regime curve] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 12/12 in VECTOR_ELT --- Backtrace: ▆ 1. ├─...[] 2. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'obic_workability.Rmd' failed with diagnostics: attempt access index 12/12 in VECTOR_ELT --- failed re-building 'obic_workability.Rmd' SUMMARY: processing the following files failed: 'obic_introduction.Rmd' 'obic_score_aggregation.Rmd' 'obic_workability.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 4.0.0
Check: installed package size
Result: NOTE installed size is 7.4Mb sub-directories of 1Mb or more: data 5.5Mb doc 1.4Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64