* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.4/phyloclim.Rcheck’
* using R version 4.4.0 alpha (2024-03-31 r86238)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.4
* using session charset: UTF-8
* checking for file ‘phyloclim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phyloclim’ version ‘0.9.5’
* package encoding: UTF-8
* 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 ‘phyloclim’ can be installed ... [10s/11s] OK
See 'https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/phyloclim-00install.html' for details.
* checking installed package size ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [7s/8s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... 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 examples ... [14s/11s] ERROR
Running examples in ‘phyloclim-Ex.R’ failed
The error most likely occurred in:

> ### Name: hypothesis.testing
> ### Title: Niche Equivalency and Background Similarity Test
> ### Aliases: niche.equivalency.test niche.identity.test identity.test
> ###   bg.similarity.test print.ntest plot.ntest
> 
> ### ** Examples
> 
> # path to MAXENT
> # --------------
> maxent.exe <- paste(system.file(package="dismo"), 
+ "/java/maxent.jar", sep = "")
> 
> # a data frame of coordinates where two species 
> # have been detected ('presence points') and
> # a raster stack of environmental covariables
> # --------------------------------------
> species <- c("enneaphylla", "laciniata")
> data(sites)
> samples <- sites[grep(paste(species, collapse = "|"), sites$spec), ]
> data.path <- system.file("extdata", package = "phyloclim")
> preds <- list.files(path = data.path, pattern = "[.]asc")
> preds <- paste(data.path, preds, sep = "/")
> preds <- stack(lapply(X = preds, FUN = raster))
> 
> # testing against 9 permutations of the data
> # -------------------------------------------
> reps <- 9
> 
> # run hypothesis tests
> # --------------------
> if (file.exists(maxent.exe)){
+   net <- niche.equivalency.test(samples, preds, reps, maxent.exe)
+   net; plot(net)
+   bst <- bg.similarity.test(samples, preds, reps, app = maxent.exe)
+   bst; plot(bst)
+ } else {
+   message("get a copy of MAXENT (see Details)")
+ }
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGILL (0x4) at pc=0x00000001281aaf78, pid=48785, tid=75527
#
# JRE version: OpenJDK Runtime Environment Temurin-11.0.22+7 (11.0.22+7) (build 11.0.22+7)
# Java VM: OpenJDK 64-Bit Server VM Temurin-11.0.22+7 (11.0.22+7, mixed mode, tiered, compressed oops, g1 gc, bsd-aarch64)
# Problematic frame:
# C  [libawt.dylib+0x2ef78]  drawAAPgram+0x248
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Volumes/Builds/packages/big-sur-arm64/results/4.4/phyloclim.Rcheck/hs_err_pid48785.log
#
# If you would like to submit a bug report, please visit:
#   https://github.com/adoptium/adoptium-support/issues
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Warning in file(fname, "r") :
  cannot open file 'R.phyloclim.temp/out/enneaphylla_proj.asc': No such file or directory
Error in file(fname, "r") : cannot open the connection
Calls: niche.equivalency.test -> read.asciigrid -> file
Execution halted
* checking PDF version of manual ... [4s/5s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:34