- 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 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 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 '