- 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 the install log 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 '