* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/FORTLS.Rcheck’
* using R Under development (unstable) (2025-06-09 r88292)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-19) 14.2.0
    GNU Fortran (Debian 14.2.0-19) 14.2.0
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* using option ‘--run-donttest’
* checking for file ‘FORTLS/DESCRIPTION’ ... OK
* this is package ‘FORTLS’ version ‘1.5.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/8s] NOTE
Maintainer: ‘Juan Alberto Molina-Valero <jamolinavalero@gmail.com>’

Found the following (possibly) invalid file URIs:
  URI: www.czu.cz/en
    From: README.md
  URI: adaptbrdy.czu.cz/en
    From: README.md
* 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 ‘FORTLS’ can be installed ... [38s/39s] OK
* used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/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 ... [16s/16s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20m/19m] ERROR
Running examples in ‘FORTLS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tree.detection.multi.scan
> ### Title: Tree-Level Variables Estimation
> ### Aliases: tree.detection.multi.scan
> 
> ### ** Examples
> 
> 
> ## No test: 
> 
> # Establishment of working directories (optional)
> # By default here we propose the current working directory of the R process
> 
> dir.data <- getwd()
> dir.result <- getwd()
> 
> 
> # Loading example data of TLS multi-scan approach point cloud (LAZ file) to dir.data
> 
> download.file(
+ "www.dropbox.com/scl/fi/es5pfj87wj0g6y8414dpo/PiceaAbies.laz?rlkey=ayt21mbndc6i6fyiz2e7z6oap&dl=1",
+               destfile = file.path(dir.data, "PiceaAbies.laz"),
+               mode = "wb")
trying URL 'www.dropbox.com/scl/fi/es5pfj87wj0g6y8414dpo/PiceaAbies.laz?rlkey=ayt21mbndc6i6fyiz2e7z6oap&dl=1'
Content type 'application/binary' length 12898220 bytes (12.3 MB)
==================================================
downloaded 12.3 MB

> 
> # Normalizing the whole point cloud data without considering arguments
> 
> pcd <- normalize(las = "PiceaAbies.laz",
+ 
+                  id = "PiceaAbies",
+ 
+                  scan.approach = "multi",
+ 
+                  voxel_size = 0.01,
+ 
+                  dir.data = dir.data, dir.result = dir.result)

                                                                                
/home/hornik/tmp/CRAN_special_donttest/FORTLS.Rcheck/FORTLS/python/voxel_grid_downsampling.py:7: RuntimeWarning: invalid value encountered in cast
  voxel_coord = tuple(np.floor(point / voxel_size).astype(int))
> 
> 
> # Tree detection without considering arguments
> 
> tree.tls <- tree.detection.multi.scan(data = pcd,
+ 
+                                       tls.precision = 0.05,
+ 
+                                       slice = 0.2,
+ 
+                                       threads = 2,
+ 
+                                       dir.result = dir.result)
Application of Statistical Outlier Removal (SOR) to the entire point cloud
Retention of points with high verticality values
Detection of tree stem axes
Computing sections

 *** caught segfault ***
address 0x55fc12c666d4, cause 'memory not mapped'

Traceback:
 1: dbscan_int(x, as.double(eps), as.integer(minPts), as.double(weights),     as.integer(borderPoints), as.integer(search), as.integer(bucketSize),     as.integer(splitRule), as.double(approx), frNN)
 2: dbscan::dbscan(.cut[, c("x", "y"), drop = FALSE], eps = .eps,     minPts = 10)
 3: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
 4: suppressMessages(dbscan::dbscan(.cut[, c("x", "y"), drop = FALSE],     eps = .eps, minPts = 10))
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
 9: try(suppressMessages(dbscan::dbscan(.cut[, c("x", "y"), drop = FALSE],     eps = .eps, minPts = 10)))
10: tree.detection.multi.scan(data = pcd, tls.precision = 0.05, slice = 0.2,     threads = 2, dir.result = dir.result)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [4s/4s] OK
  Running ‘testthat.R’ [4s/4s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [209s/154s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘1.txt’ ‘2.txt’ ‘PiceaAbies.laz’ ‘PiceaAbies.txt’ ‘PinusRadiata.laz’
  ‘PinusRadiata.txt’ ‘RB.G.angle.count.html’ ‘RB.G.fixed.area.html’
  ‘RB.G.k.tree.html’ ‘RB.N.angle.count.html’ ‘RB.N.fixed.area.html’
  ‘RB.N.k.tree.html’ ‘RB.V.angle.count.html’ ‘RB.angle.count.csv’
  ‘RB.d.angle.count.html’ ‘RB.d.fixed.area.html’ ‘RB.d.k.tree.html’
  ‘RB.fixed.area.csv’ ‘RB.h.angle.count.html’ ‘RB.h.fixed.area.html’
  ‘RB.h.k.tree.html’ ‘RB.k.tree.csv’
  ‘metrics.variables.angle.count.plot.csv’
  ‘metrics.variables.fixed.area.plot.csv’
  ‘metrics.variables.k.tree.plot.csv’
  ‘opt.correlations.angle.count.pearson.html’
  ‘opt.correlations.angle.count.spearman.html’
  ‘opt.correlations.fixed.area.pearson.html’
  ‘opt.correlations.fixed.area.spearman.html’
  ‘opt.correlations.k.tree.pearson.html’
  ‘opt.correlations.k.tree.spearman.html’
  ‘simulations.angle.count.plot.csv’ ‘simulations.fixed.area.plot.csv’
  ‘simulations.k.tree.plot.csv’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs