• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘lidR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘lidR’ version ‘4.2.2’
• 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 ‘lidR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
• checking C++ specification ... OK
• 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 ... [5s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/5s] OK
• checking loading without being on the library search path ... [4s/5s] OK
• checking whether startup messages can be suppressed ... [4s/5s] 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 ... [40s/46s] 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... NOTE File ‘lidR/libs/lidR.so’:   Found non-API call to R: ‘ATTRIB’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [6s/6s] ERROR Running examples in ‘lidR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: aggregate > ### Title: Metric derivation at different levels of regularization > ### Aliases: aggregate cloud_metrics crown_metrics hexagon_metrics > ### pixel_metrics plot_metrics polygon_metrics template_metrics > ### voxel_metrics > > ### ** Examples > > LASfile <- system.file("extdata", "Megaplot.laz", package="lidR") > las <- readLAS(LASfile, filter = "-keep_random_fraction 0.5")                                                                                  > col <- sf::sf.colors(15) > fun1 <- ~list(maxz = max(Z)) > fun2 <- ~list(q85 = quantile(Z, probs = 0.85)) > > set_lidr_threads(1) ; data.table::setDTthreads(1) # for cran only > > # ================ > # CLOUD METRICS > # ================ > > cloud_metrics(las, .stdmetrics_z) $zmax [1] 29.11 $zmean [1] 13.27629 $zsd [1] 7.456352 $zskew [1] -0.4764641 $zkurt [1] 2.086569 $zentropy [1] 0.9034754 $pzabovezmean [1] 57.36855 $pzabove2 [1] 85.71007 $zq5 [1] 0 $zq10 [1] 0.09 $zq15 [1] 2.86 $zq20 [1] 5.79 $zq25 [1] 7.81 $zq30 [1] 9.64 $zq35 [1] 11.21 $zq40 [1] 12.63 $zq45 [1] 13.83 $zq50 [1] 14.91 $zq55 [1] 16 $zq60 [1] 16.89 $zq65 [1] 17.71 $zq70 [1] 18.53 $zq75 [1] 19.3 $zq80 [1] 20.09 $zq85 [1] 20.88 $zq90 [1] 21.79 $zq95 [1] 23.05 $zpcum1 [1] 6.52697 $zpcum2 [1] 12.03731 $zpcum3 [1] 20.22982 $zpcum4 [1] 30.04461 $zpcum5 [1] 43.09585 $zpcum6 [1] 59.87833 $zpcum7 [1] 80.14871 $zpcum8 [1] 95.21968 $zpcum9 [1] 99.55928 > > # ================ > # PIXEL METRICS > # ================ > > m <- pixel_metrics(las, fun1, 20) > #plot(m, col = col) > > # ================ > # PLOT METRICS > # ================ > > shpfile <- system.file("extdata", "efi_plot.shp", package="lidR") > inventory <- sf::st_read(shpfile, quiet = TRUE) > inventory # contains an ID and a Value Of Interest (VOI) per plot Simple feature collection with 5 features and 2 fields Geometry type: POINT Dimension: XY Bounding box: xmin: 684838.9 ymin: 5017796 xmax: 684976.6 ymax: 5017958 Projected CRS: NAD83 / UTM zone 17N   IDPEP VOI geometry 1 PEPQ1 14.157140 POINT (684976.6 5017821) 2 PEPQ2 12.720584 POINT (684923.9 5017958) 3 PEPQ3 11.396656 POINT (684838.9 5017942) 4 PEPQ4 11.597471 POINT (684855 5017891) 5 PEPQ5 8.263425 POINT (684944 5017796) > > m <- plot_metrics(las, fun2, inventory, radius = 11.28) > #plot(header(las)) > #plot(m["q85"], pch = 19, cex = 3, add = TRUE) > > > # ================ > # VOXEL METRICS > # ================ > > m <- voxel_metrics(las, length(Z), 8) Error in `[.data.table`(by, , `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", :   attempt access index 3/3 in VECTOR_ELT Calls: voxel_metrics -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [102s/115s] ERROR   Running ‘testthat.R’ [102s/114s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > Sys.setenv("R_TESTS" = "")   >   > library(testthat)   > library(lidR)   > test_check("lidR")   Tests using raster: terra   Tests using future: TRUE   Tests using OpenMP thread: 1   Tests using rlas: 1.8.2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   OGR: Unsupported geometry type   OGR: Unsupported geometry type                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Chunk 1 of 1 (100%): state ✓                                                                                         Saving _problems/test-metrics_voxels-5.R   Saving _problems/test-metrics_voxels-14.R   Saving _problems/test-metrics_voxels-23.R                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 [ FAIL 3 | WARN 0 | SKIP 46 | PASS 1289 ]      ══ Skipped tests (46) ══════════════════════════════════════════════════════════   • On CRAN (41): 'test-apply_automerge.R:99:3', 'test-apply_automerge.R:163:3',     'test-apply_automerge.R:183:3', 'test-apply_automerge.R:196:3',     'test-apply_automerge.R:217:3', 'test-apply_automerge.R:229:3',     'test-apply_automerge.R:263:3', 'test-apply_automerge.R:274:3',     'test-apply_automerge.R:320:3', 'test-apply_automerge.R:335:3',     'test-apply_autoread.R:3:3', 'test-apply_generic.R:22:3',     'test-apply_generic.R:108:3', 'test-catalog_laxindex.R:4:3',     'test-classify_ground.R:62:3', 'test-classify_poi.R:21:3',     'test-concaveman.R:15:3', 'test-concaveman.R:64:3',     'test-fullwaveform.R:2:3', 'test-generic_local_maximum.R:2:3',     'test-metrics_crowns.R:31:3', 'test-metrics_crowns.R:112:3',     'test-metrics_crowns.R:122:3', 'test-plot.R:7:3', 'test-plot.R:15:3',     'test-plot.R:49:3', 'test-plot.R:73:3', 'test-plot.R:79:3',     'test-plot.R:86:3', 'test-plot.R:93:3', 'test-plot.R:100:3',     'test-plot.R:107:3', 'test-plot.R:118:3', 'test-projection.R:82:3',     'test-projection.R:107:3', 'test-rasterize_canopy.R:66:3',     'test-rasterize_terrain.R:145:3', 'test-segment_snags.R:27:2',     'test-segment_trees.R:73:3', 'test-track_sensor.R:45:3',     'test-voxelize_points.R:15:3'   • Point metrics disable (1): 'test-segment_shape.R:51:3'   • Point metrics disabled (1): 'test-metrics_points.R:9:1'   • empty test (3): , ,      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-metrics_voxels.R:5:3'): voxel_metrics returns a named data.frame ──   Error in ``[.data.table`(by, , `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid"))`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─lidR::voxel_metrics(las, list(Imean = mean(Intensity)), 5) at test-metrics_voxels.R:5:3    2. ├─by[, `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid")]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-metrics_voxels.R:14:3'): voxel_metrics works with all_voxels ───   Error in ``[.data.table`(by, , `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid"))`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─lidR::voxel_metrics(las, list(Imean = mean(Intensity)), 5, all_voxels = TRUE) at test-metrics_voxels.R:14:3    2. ├─by[, `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid")]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-metrics_voxels.R:23:3'): voxel_metrics accepts both an expression or a formula ──   Error in ``[.data.table`(by, , `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid"))`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─lidR::voxel_metrics(las, list(Imean = mean(Intensity)), 5) at test-metrics_voxels.R:23:3    2. ├─by[, `:=`(GRP, .GRP), by = c("Xgrid", "Ygrid", "Zgrid")]    3. └─data.table:::`[.data.table`(...)      [ FAIL 3 | WARN 0 | SKIP 46 | PASS 1289 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [38s/51s] OK
• checking PDF version of manual ... [7s/10s] OK
• checking HTML version of manual ... [6s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE