CRAN Package Check Results for Package phyloclim

Last updated on 2024-05-27 12:51:39 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.5 36.87 300.55 337.42 OK
r-devel-linux-x86_64-debian-gcc 0.9.5 22.62 215.01 237.63 OK
r-devel-linux-x86_64-fedora-clang 0.9.5 404.33 OK
r-devel-linux-x86_64-fedora-gcc 0.9.5 564.29 OK
r-devel-windows-x86_64 0.9.5 24.00 177.00 201.00 OK
r-patched-linux-x86_64 0.9.5 25.29 285.05 310.34 OK
r-release-linux-x86_64 0.9.5 33.48 277.75 311.23 OK
r-release-macos-arm64 0.9.5 94.00 ERROR
r-release-windows-x86_64 0.9.5 24.00 179.00 203.00 OK
r-oldrel-macos-arm64 0.9.5 149.00 OK
r-oldrel-macos-x86_64 0.9.5 360.00 ERROR
r-oldrel-windows-x86_64 0.9.5 33.00 243.00 276.00 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)") + } # # 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 Flavor: r-release-macos-arm64

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-oldrel-macos-x86_64