CRAN Package Check Results for Package phyloclim

Last updated on 2021-06-19 23:49:28 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.5 9.36 89.71 99.07 OK
r-devel-linux-x86_64-debian-gcc 0.9.5 8.14 68.74 76.88 OK
r-devel-linux-x86_64-fedora-clang 0.9.5 127.19 OK
r-devel-linux-x86_64-fedora-gcc 0.9.5 327.63 OK
r-devel-windows-x86_64 0.9.5 15.00 109.00 124.00 OK
r-devel-windows-x86_64-gcc10-UCRT 0.9.5 OK
r-patched-linux-x86_64 0.9.5 10.07 86.12 96.19 OK
r-patched-solaris-x86 0.9.5 165.30 OK
r-release-linux-x86_64 0.9.5 10.59 87.04 97.63 OK
r-release-macos-arm64 0.9.5 ERROR
r-release-macos-x86_64 0.9.5 ERROR
r-release-windows-ix86+x86_64 0.9.5 21.00 108.00 129.00 OK
r-oldrel-macos-x86_64 0.9.5 OK
r-oldrel-windows-ix86+x86_64 0.9.5 16.00 107.00 123.00 OK

Additional issues

M1mac

Check Details

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
Flavors: r-release-macos-arm64, r-release-macos-x86_64