* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/phyloclim.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84266)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.3
* 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 ... [16s/56s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/13s] OK
* checking whether the package can be unloaded cleanly ... [5s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/14s] OK
* checking loading without being on the library search path ... [5s/13s] 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 ... [12s/31s] OK
* checking Rd files ... [0s/1s] 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 ... [9s/22s] 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)")
+ }
Exception in thread "AWT-EventQueue-0" java.awt.HeadlessException
	at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
	at java.desktop/java.awt.Window.<init>(Window.java:548)
	at java.desktop/java.awt.Frame.<init>(Frame.java:423)
	at java.desktop/javax.swing.JFrame.<init>(JFrame.java:224)
	at density.MaxEnt.createAndShowGUI(MaxEnt.java:65)
	at density.MaxEnt.access$000(MaxEnt.java:30)
	at density.MaxEnt$1.run(MaxEnt.java:51)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
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 ... [6s/9s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 6:00