* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/spcosa.Rcheck’
* using R Under development (unstable) (2025-10-13 r88918)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘spcosa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spcosa’ version ‘0.4-5’
* 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 ‘spcosa’ can be installed ... [20s/47s] OK
* checking package 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 ... OK
* checking whether the package can be loaded with stated dependencies ... [4s/12s] OK
* checking whether the package can be unloaded cleanly ... [4s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [4s/12s] OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [20s/52s] OK
* checking Rd files ... 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 examples ... [9s/46s] ERROR
Running examples in ‘spcosa-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimate-methods
> ### Title: Estimating Statistics
> ### Aliases: estimate-methods estimate
> ###   estimate,character,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ###   estimate,character,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ###   estimate,SamplingVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ###   estimate,SamplingVariance,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ###   estimate,SpatialCumulativeDistributionFunction,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ###   estimate,SpatialMean,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ###   estimate,SpatialMean,CompactStratificationEqualArea,SamplingPatternRandomComposite,data.frame-method
> ###   estimate,SpatialVariance,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ###   estimate,StandardError,CompactStratification,SamplingPatternRandomSamplingUnits,data.frame-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Note: the example below requires the 'sf'-package.
> if (require(sf)) {
+     # read vector representation of the "Mijdrecht" area
+     shp <- as(st_read(
+         dsn = system.file("maps", package = "spcosa"),
+         layer = "mijdrecht"), "Spatial")
+ 
+     # stratify into 30 strata
+     myStratification <- stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
+ 
+     # random sampling of two sampling units per stratum
+     mySamplingPattern <- spsample(myStratification, n = 2)
+ 
+     # plot sampling pattern
+     plot(myStratification, mySamplingPattern)
+ 
+     # simulate data
+     # (in real world cases these data have to be obtained by field work etc.)
+     myData <- as(mySamplingPattern, "data.frame")
+     myData$observation <- rnorm(n = nrow(myData), mean = 10, sd = 1)
+ 
+     # design-based inference
+     estimate("spatial mean", myStratification, mySamplingPattern, myData["observation"])
+     estimate("sampling variance", myStratification, mySamplingPattern, myData["observation"])
+     estimate("standard error", myStratification, mySamplingPattern, myData["observation"])
+     estimate("spatial variance", myStratification, mySamplingPattern, myData["observation"])
+     estimate("scdf", myStratification, mySamplingPattern, myData["observation"])
+ }
Loading required package: sf
Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.2; sf_use_s2() is TRUE
Reading layer `mijdrecht' from data source 
  `/data/gannet/ripley/R/packages/tests-ATLAS/spcosa.Rcheck/spcosa/maps' 
  using driver `ESRI Shapefile'
Simple feature collection with 1 feature and 2 fields
Geometry type: POLYGON
Dimension:     XY
Bounding box:  xmin: 115796.2 ymin: 463380.5 xmax: 121670.8 ymax: 471524.6
CRS:           NA
2025-10-14 15:28:21 | optimizing configuration 1 
2025-10-14 15:28:22 |    current objective function value: 50485.85 
2025-10-14 15:28:22 |    minimum objective function value: 50485.85 
2025-10-14 15:28:22 | optimizing configuration 2 
[gannet:3386665:0:3386665] Caught signal 11 (Segmentation fault: invalid permissions for mapped object at address 0x7f4ce4dc4000)
==== backtrace (tid:3386665) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f4c298e3df4]
 1  /lib64/libucs.so.0(+0x17aed) [0x7f4c298e5aed]
 2  /lib64/libucs.so.0(+0x17cbd) [0x7f4c298e5cbd]
 3  [0x7f4cbb6501de]
=================================

 *** caught segfault ***
address 0x4d20033ad29, cause 'unknown'

Traceback:
 1: .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,     .jcast(if (inherits(o, "jobjRef") || inherits(o, "jarrayRef")) o else cl,         "java/lang/Object"), .jnew("java/lang/String", method),     j_p, j_pc, use.true.class = TRUE, evalString = simplify,     evalArray = FALSE)
 2: .jrcall(x, name, ...)
 3: p$optimize()
 4: .local(object, ...)
 5: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints,     maxIterations = maxIterations, nTry = nTry, equalArea = equalArea,     verbose = verbose)
 6: stratify(object = object, nStrata = nStrata, priorPoints = priorPoints,     maxIterations = maxIterations, nTry = nTry, equalArea = equalArea,     verbose = verbose)
 7: .local(object, ...)
 8: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
 9: stratify(shp, nStrata = 30, nTry = 10, verbose = TRUE)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTestSuite.R’ [66s/117s]
 [66s/118s] OK
* checking PDF version of manual ... [8s/16s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/spcosa.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:55.36, 195.26 + 15.00