Last updated on 2022-08-15 08:50:20 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ips | 6 | 7 | |
| phyloclim | 1 | 12 |
Current CRAN status: NOTE: 6, OK: 7
Version: 0.0.11
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘seqinr’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.9.5
Check: examples
Result: 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.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.<init>(Window.java:536)
at java.awt.Frame.<init>(Frame.java:420)
at javax.swing.JFrame.<init>(JFrame.java:233)
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.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
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
Flavor: r-oldrel-macos-x86_64