• 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 ‘BIOMASS/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘BIOMASS’ version ‘2.2.4-1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] 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 ‘BIOMASS’ 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 ... [10s/11s] OK
• checking whether the package can be loaded with stated dependencies ... [9s/12s] OK
• checking whether the package can be unloaded cleanly ... [9s/12s] OK
• checking whether the namespace can be loaded with stated dependencies ... [9s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [10s/12s] OK
• checking loading without being on the library search path ... [9s/11s] OK
• checking whether startup messages can be suppressed ... [9s/11s] 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 ... [47s/61s] 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 ... [1s/1s] 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 ... [10s/13s] ERROR Running examples in ‘BIOMASS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: check_plot_coord > ### Title: Check coordinates of plot corners and trees > ### Aliases: check_plot_coord > > ### ** Examples > > # One plot with repeated measurements of each corner > data("NouraguesPlot201") > check_plot201 <- check_plot_coord( + corner_data = NouraguesPlot201, + proj_coord = c("Xutm","Yutm"), rel_coord = c("Xfield","Yfield"), + trust_GPS_corners = TRUE, draw_plot = FALSE) Error in `[.data.table`(corner_dat, , `:=`(c("x_proj_mean", "y_proj_mean", :   attempt access index 9/9 in VECTOR_ELT Calls: check_plot_coord ... [.data.table -> check_corner_fct -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [27s/29s] ERROR   Running ‘testthat.R’ [27s/28s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(BIOMASS)   For more information on using BIOMASS, visit https://umr-amap.github.io/BIOMASS      Using temporary cache     It is recommended to use a permanent cache to avoid to re-download files on each session.     See function createCache() or BIOMASS.cache option.   >   > test_check("BIOMASS")   Saving _problems/test-AGBmonteCarlo-289.R   Saving _problems/test-check_coord_plot-85.R   Saving _problems/test-check_coord_plot-96.R   Saving _problems/test-dividePlot-7.R   Saving _problems/test-retrieveH-77.R   Saving _problems/test-small_function-242.R   Saving _problems/test-subplot_summary-7.R   [ FAIL 7 | WARN 0 | SKIP 17 | PASS 359 ]      ══ Skipped tests (17) ══════════════════════════════════════════════════════════   • On CRAN (17): 'test-AGBmonteCarlo.R:153:3', 'test-check_coord_plot.R:106:3',     'test-check_coord_plot.R:124:3', 'test-computeAGB.R:43:3',     'test-correctTaxo.R:5:3', 'test-modelHD.R:120:3', 'test-retrieveH.R:36:3',     'test-small_function.R:22:3', 'test-small_function.R:38:3',     'test-small_function.R:102:3', 'test-small_function.R:112:3',     'test-small_function.R:124:3', 'test-small_function.R:140:5',     'test-small_function.R:140:5', 'test-small_function.R:140:5',     'test-small_function.R:140:5', 'test-small_function.R:162:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-AGBmonteCarlo.R:289:3'): With the plot value ───────────────────   Error in ``[.data.table`(data, , `:=`(H, predictHeight(D, model = model[[unique(plot)]], err)), by = plot)`: attempt access index 2/2 in VECTOR_ELT   Backtrace:       ▆    1. └─BIOMASS::AGBmonteCarlo(...) at test-AGBmonteCarlo.R:289:3    2. └─base::apply(...)    3. └─BIOMASS (local) FUN(newX[, i], ...)    4. └─BIOMASS::predictHeight(x, model = HDmodel, err = TRUE, plot = plot)    5. ├─...[]    6. └─data.table:::`[.data.table`(...)   ── Error ('test-check_coord_plot.R:85:3'): check_plot_coord in long lat ────────   Error in ``[.data.table`(coord, , `:=`(c("X", "Y"), proj4::project(.(long, lat), proj = unique(.BY))), by = codeUTM)`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. ├─BIOMASS::check_plot_coord(...) at test-check_coord_plot.R:85:3    2. │ ├─corner_dt[, latlong2UTM_fct(.SD), by = plot_ID, .SDcols = colnames(corner_dt)]    3. │ └─data.table:::`[.data.table`(...)    4. └─BIOMASS (local) latlong2UTM_fct(.SD)    5. └─BIOMASS::latlong2UTM(dat[, c("long", "lat")])    6. ├─...[]    7. └─data.table:::`[.data.table`(...)   ── Error ('test-check_coord_plot.R:94:3'): check_plot_coord, trust_GPS_corners ──   Error in ``[.data.table`(corner_dat, , `:=`(c("x_proj_mean", "y_proj_mean", "row_number"), list(mean(x_proj), mean(y_proj), .I)), by = list(x_rel, y_rel))`: attempt access index 9/9 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_warning(...) at test-check_coord_plot.R:94:3     2. │ └─testthat:::quasi_capture(...)     3. │ ├─testthat (local) .capture(...)     4. │ │ └─base::withCallingHandlers(...)     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     6. ├─BIOMASS::check_plot_coord(...)     7. │ ├─corner_dt[, check_corner_fct(.SD), by = plot_ID, .SDcols = colnames(corner_dt)]     8. │ └─data.table:::`[.data.table`(...)     9. └─BIOMASS (local) check_corner_fct(.SD)    10. ├─...[]    11. └─data.table:::`[.data.table`(...)   ── Error ('test-dividePlot.R:7:1'): (code run outside of `test_that()`) ────────   Error in ``[.data.table`(corner_dat, , `:=`(c("x_proj_mean", "y_proj_mean", "row_number"), list(mean(x_proj), mean(y_proj), .I)), by = list(x_rel, y_rel))`: attempt access index 9/9 in VECTOR_ELT   Backtrace:       ▆    1. ├─base::suppressWarnings(...) at test-dividePlot.R:7:1    2. │ └─base::withCallingHandlers(...)    3. ├─BIOMASS::check_plot_coord(...)    4. │ ├─corner_dt[, check_corner_fct(.SD), by = plot_ID, .SDcols = colnames(corner_dt)]    5. │ └─data.table:::`[.data.table`(...)    6. └─BIOMASS (local) check_corner_fct(.SD)    7. ├─...[]    8. └─data.table:::`[.data.table`(...)   ── Error ('test-retrieveH.R:77:3'): With the plot ──────────────────────────────   Error in ``[.data.table`(data, , `:=`(H, predictHeight(D, model = model[[unique(plot)]], err)), by = plot)`: attempt access index 2/2 in VECTOR_ELT   Backtrace:       ▆    1. └─BIOMASS::retrieveH(D, model, plot = NouraguesHD$plotId) at test-retrieveH.R:77:3    2. └─BIOMASS::predictHeight(D, model, plot = plot)    3. ├─...[]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-small_function.R:242:3'): lat long to UTM ──────────────────────   Error in ``[.data.table`(coord, , `:=`(c("X", "Y"), proj4::project(.(long, lat), proj = unique(.BY))), by = codeUTM)`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─BIOMASS::latlong2UTM(coord) at test-small_function.R:242:3    2. ├─...[]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-subplot_summary.R:7:1'): (code run outside of `test_that()`) ───   Error in ``[.data.table`(corner_dat, , `:=`(c("x_proj_mean", "y_proj_mean", "row_number"), list(mean(x_proj), mean(y_proj), .I)), by = list(x_rel, y_rel))`: attempt access index 9/9 in VECTOR_ELT   Backtrace:       ▆    1. ├─base::suppressWarnings(...) at test-subplot_summary.R:7:1    2. │ └─base::withCallingHandlers(...)    3. ├─BIOMASS::check_plot_coord(...)    4. │ ├─corner_dt[, check_corner_fct(.SD), by = plot_ID, .SDcols = colnames(corner_dt)]    5. │ └─data.table:::`[.data.table`(...)    6. └─BIOMASS (local) check_corner_fct(.SD)    7. ├─...[]    8. └─data.table:::`[.data.table`(...)      [ FAIL 7 | WARN 0 | SKIP 17 | PASS 359 ]   Deleting unused snapshots:   'subplot_summary/subplot-summary-multiple-metrics-204.svg',   'subplot_summary/subplot-summary-multiple-plot-201.svg',   'subplot_summary/subplot-summary-multiple-plot-204.svg',   'subplot_summary/subplot-summary-proj-coords.svg',   'subplot_summary/subplot-summary-quantile.svg', and   'subplot_summary/subplot-summary-rel-coords.svg'   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [37s/55s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Vignette_BIOMASS.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Vignette_BIOMASS.Rmd’ --- re-building ‘Vignette_spatialized_trees_and_forest_stand_metrics.Rmd’ using rmarkdown Quitting from Vignette_spatialized_trees_and_forest_stand_metrics.Rmd:105-113 [check_plot_trust_GPS] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 3/3 in VECTOR_ELT --- Backtrace:     ▆  1. ├─BIOMASS::check_plot_coord(...)  2. │ ├─corner_dt[, latlong2UTM_fct(.SD), by = plot_ID, .SDcols = colnames(corner_dt)]  3. │ └─data.table:::`[.data.table`(...)  4. └─BIOMASS (local) latlong2UTM_fct(.SD)  5. └─BIOMASS::latlong2UTM(dat[, c("long", "lat")])  6. ├─...[]  7. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Vignette_spatialized_trees_and_forest_stand_metrics.Rmd' failed with diagnostics: attempt access index 3/3 in VECTOR_ELT --- failed re-building ‘Vignette_spatialized_trees_and_forest_stand_metrics.Rmd’ SUMMARY: processing the following file failed:   ‘Vignette_spatialized_trees_and_forest_stand_metrics.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [6s/9s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs