CRAN Package Check Results for Package phyloclim

Last updated on 2024-02-20 19:51:12 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.5 OK
r-devel-linux-x86_64-debian-gcc 0.9.5 24.52 211.95 236.47 OK
r-devel-linux-x86_64-fedora-clang 0.9.5 402.12 OK
r-devel-linux-x86_64-fedora-gcc 0.9.5 560.44 OK
r-devel-windows-x86_64 0.9.5 25.00 179.00 204.00 OK
r-patched-linux-x86_64 0.9.5 33.69 279.97 313.66 OK
r-release-linux-x86_64 0.9.5 27.86 278.85 306.71 OK
r-release-macos-arm64 0.9.5 149.00 OK
r-release-macos-x86_64 0.9.5 360.00 ERROR
r-release-windows-x86_64 0.9.5 32.00 236.00 268.00 OK
r-oldrel-macos-arm64 0.9.5 126.00 OK
r-oldrel-windows-x86_64 0.9.5 34.00 232.00 266.00 OK

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.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 Flavor: r-release-macos-x86_64