- using R version 3.5.3 (2019-03-11)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'SDMtune/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'SDMtune' version '0.2.1'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'SDMtune' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking 'build' 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- loading checks for arch 'i386'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- loading checks for arch 'x64'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... 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 ... [19s] OK
- checking Rd files ... 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 contents of 'data' directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking R/sysdata.rda ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ...
- running examples for arch 'i386' ... ERROR
Running examples in 'SDMtune-Ex.R' failed
The error most likely occurred in:
> ### Name: aicc
> ### Title: AICc
> ### Aliases: aicc
>
> ### ** Examples
>
> # Acquire environmental variables
> files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
+ pattern = "grd", full.names = TRUE)
> predictors <- raster::stack(files)
>
> # Prepare presence and background locations
> p_coords <- virtualSp$presence
> bg_coords <- virtualSp$background
>
> # Create SWD object
> data <- prepareSWD(species = "Virtual species", p = p_coords, a = bg_coords,
+ env = predictors, categorical = "biome")
Extracting predictor information for presence locations...
Extracting predictor information for absence/background locations...
>
> # Train a model
> model <- train(method = "Maxnet", data = data, fc = "l")
Error in get(fun, mode = "function", envir = parent.frame()) :
object 'trainMaxnet' of mode 'function' was not found
Calls: train -> do.call -> %in% -> formalArgs -> formals -> get
Execution halted
- running examples for arch 'x64' ... ERROR
Running examples in 'SDMtune-Ex.R' failed
The error most likely occurred in:
> ### Name: aicc
> ### Title: AICc
> ### Aliases: aicc
>
> ### ** Examples
>
> # Acquire environmental variables
> files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
+ pattern = "grd", full.names = TRUE)
> predictors <- raster::stack(files)
>
> # Prepare presence and background locations
> p_coords <- virtualSp$presence
> bg_coords <- virtualSp$background
>
> # Create SWD object
> data <- prepareSWD(species = "Virtual species", p = p_coords, a = bg_coords,
+ env = predictors, categorical = "biome")
Extracting predictor information for presence locations...
Extracting predictor information for absence/background locations...
>
> # Train a model
> model <- train(method = "Maxnet", data = data, fc = "l")
Error in get(fun, mode = "function", envir = parent.frame()) :
object 'trainMaxnet' of mode 'function' was not found
Calls: train -> do.call -> %in% -> formalArgs -> formals -> get
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ...
- running tests for arch 'i386' ... [24s] ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [22s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SDMtune)
_____ ____ __ ___ __
/ ___/ / __ \ / |/ // /_ __ __ ____ ___
\__ \ / / / // /|_/ // __// / / // __ \ / _ \
___/ // /_/ // / / // /_ / /_/ // / / // __/
/____//_____//_/ /_/ \__/ \__,_//_/ /_/ \___/ version 0.2.1
To cite this package in publications type: citation("SDMtune").
>
> test_check("SDMtune")
-- 1. Error: (unknown) (@test-utils.R#5) --------------------------------------
object 'trainANN' of mode 'function' was not found
Backtrace:
1. SDMtune::train("ANN", data = data, size = 10)
4. methods::formalArgs(f)
5. base::formals(def)
6. base::get(fun, mode = "function", envir = parent.frame())
== testthat results ===========================================================
[ OK: 353 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 1 ]
1. Error: (unknown) (@test-utils.R#5)
Error: testthat unit tests failed
Execution halted
- running tests for arch 'x64' ... [25s] ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(SDMtune)
_____ ____ __ ___ __
/ ___/ / __ \ / |/ // /_ __ __ ____ ___
\__ \ / / / // /|_/ // __// / / // __ \ / _ \
___/ // /_/ // / / // /_ / /_/ // / / // __/
/____//_____//_/ /_/ \__/ \__,_//_/ /_/ \___/ version 0.2.1
To cite this package in publications type: citation("SDMtune").
>
> test_check("SDMtune")
-- 1. Error: (unknown) (@test-utils.R#5) --------------------------------------
object 'trainANN' of mode 'function' was not found
Backtrace:
1. SDMtune::train("ANN", data = data, size = 10)
4. methods::formalArgs(f)
5. base::formals(def)
6. base::get(fun, mode = "function", envir = parent.frame())
== testthat results ===========================================================
[ OK: 353 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 1 ]
1. Error: (unknown) (@test-utils.R#5)
Error: testthat unit tests failed
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [5s] OK
- checking PDF version of manual ... OK
- DONE
Status: 4 ERRORs