- using R Under development (unstable) (2025-01-24 r87627)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘ENMTools/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘ENMTools’ version ‘1.1.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘ENMTools’ can be installed ... [16s/17s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [3s/4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
- checking whether the package can be unloaded cleanly ... [4s/4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
- checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
- checking loading without being on the library search path ... [4s/4s] OK
- checking whether startup messages can be suppressed ... [3s/4s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [9s/9s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking R/sysdata.rda ... OK
- checking examples ... [7s/6s] ERROR
Running examples in ‘ENMTools-Ex.R’ failed
The error most likely occurred in:
> ### Name: enmtools.maxent
> ### Title: Takes an emtools.species object with presence and background
> ### points, and builds a maxent model
> ### Aliases: enmtools.maxent
>
> ### ** Examples
>
> if(check.extras("enmtools.maxent")) {
+ ## maxent is not working on some platforms so use try()
+ try(enmtools.maxent(iberolacerta.clade$species$monticola, env = euro.worldclim))
+ }
*** caught illegal operation ***
address 0x106286f78, cause 'illegal trap'
Traceback:
1: rJava::.jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, "-s", pfn, args))
2: .local(x, p, ...)
3: maxent(x, p, ...)
4: maxent(x, p, ...)
5: .local(x, p, ...)
6: dismo::maxent(raster::stack(env), p = analysis.df[analysis.df$presence == 1, 1:2], a = analysis.df[analysis.df$presence == 0, 1:2], ...)
7: dismo::maxent(raster::stack(env), p = analysis.df[analysis.df$presence == 1, 1:2], a = analysis.df[analysis.df$presence == 0, 1:2], ...)
8: withVisible(...elt(i))
9: capture.output(this.mx <- dismo::maxent(raster::stack(env), p = analysis.df[analysis.df$presence == 1, 1:2], a = analysis.df[analysis.df$presence == 0, 1:2], ...))
10: enmtools.maxent(iberolacerta.clade$species$monticola, env = euro.worldclim)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
15: try(enmtools.maxent(iberolacerta.clade$species$monticola, env = euro.worldclim))
An irrecoverable exception occurred. R is aborting now ...
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [24s/24s] OK
Running ‘testthat.R’ [24s/24s]
- checking PDF version of manual ... [3s/3s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '