Last updated on 2024-07-24 12:21:19 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ips | 2 | 11 | |
| phyloclim | 2 | 11 |
Current CRAN status: NOTE: 2, OK: 11
Version: 0.0.12
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
DNAbin2index.Rd: DNAbin
EmptyCells.Rd: DNAbin
code.simple.gaps.Rd: DNAbin
collapseUnsupportedEdges.Rd: phylo
combMyTree.Rd: phylo
del.miss.Rd: DNAbin
deleteGaps.Rd: DNAbin
fixNodes.Rd: phylo, read.nexus
forceEqualTipHeights.Rd: is.ultrametric, chronos
index2DNAbin.Rd: DNAbin
ips-package.Rd: ladderize, rotate
ips.16S.Rd: DNAbin
ips.28S.Rd: DNAbin
ips.cox1.Rd: DNAbin
mafft.Rd: phylo
mafft.merge.Rd: DNAbin, AAbin, phylo
mrbayes.Rd: DNAbin
multistate.Rd: ace
neighboringPairs.Rd: mst
ntip.Rd: phylo
pathd8.Rd: phylo
phylo2mafft.Rd: phylo
phylo2mst.Rd: phylo
pis.Rd: DNAbin
raxml.Rd: DNAbin, phylo
raxml.partitions.Rd: DNAbin, cbind.DNAbin
rbeauti.Rd: DNAbin
read.Rd: cbind.DNAbin
sister.Rd: phylo
splitIntoClades.Rd: phylo
terminalSisters.Rd: phylo
tipHeights.Rd: phylo, branching.times
traitRate.Rd: phylo, DNAbin, read.tree
write.fas.Rd: DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Current CRAN status: ERROR: 2, OK: 11
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