• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘OBIC/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘OBIC’ version ‘4.0.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘OBIC’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [21s/27s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [4s/5s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/2s] ERROR Running examples in ‘OBIC-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [11s/13s] ERROR   Running ‘testthat.R’ [10s/13s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/32s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘description-of-the-columns.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace:      ▆   1. ├─base::grep("I_C_", names(obic_field_dt(binnenveld[ID == 1], output = "indicators")))   2. │ └─base::is.factor(x)   3. └─OBIC::obic_field_dt(binnenveld[ID == 1], output = "indicators")   4. └─OBIC::obic_field(...)   5. ├─dt[, `:=`(D_GA, calc_grass_age(ID, B_LU_BRP))]   6. └─data.table:::`[.data.table`(...)   7. └─base::eval(jsub, SDenv, parent.frame())   8. └─base::eval(jsub, SDenv, parent.frame())   9. └─OBIC::calc_grass_age(ID, B_LU_BRP)  10. ├─dt[, `:=`(grass_age, rev(cumsum(grass))), by = rleid(ID, grass)]  11. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- 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
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [6s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs