* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/MaxentVariableSelection.Rcheck’
* using R Under development (unstable) (2024-03-16 r86144)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
    GNU Fortran (GCC) 13.2.1 20231011 (Red Hat 13.2.1-4)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘MaxentVariableSelection/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MaxentVariableSelection’ version ‘1.0-3’
* 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 ‘MaxentVariableSelection’ can be installed ... 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) MaxentVariableSelection-package.Rd:46: Lost braces; missing escapes or markup?
    46 | \tab Tyberghein L, Verbruggen H, Pauly K, Troupin C, Mineur F and {De Clerck}, O (2012)\cr
       |                                                                   ^
* checking Rd metadata ... OK
* checking Rd line widths ... 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘MaxentVariableSelection-Ex.R’ failed
The error most likely occurred in:

> ### Name: VariableSelection
> ### Title: Selecting the best set of relevant environmental variables along
> ###   with the optimal regularization multiplier for Maxent Niche Modeling
> ### Aliases: VariableSelection
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Please find a workflow tutorial in the vignette of this package. It
> ##D # will guide you through the settings and usage of the
> ##D # 'VariableSelection' function, the core function of this package.
> ## End(Not run)
> ## No test: 
> VariableSelection(
+ maxent="C:/.../maxent.jar",
+ outdir="OutputDirectory",
+ gridfolder="BioORACLEVariables",
+ occurrencelocations=system.file("extdata", "Occurrencedata.csv", package="MaxentVariableSelection"),
+ backgroundlocations=system.file("extdata", "Backgrounddata.csv", package="MaxentVariableSelection"),
+ additionalargs="nolinear noquadratic noproduct nothreshold noautofeature",
+ contributionthreshold=5,
+ correlationthreshold=0.9,
+ betamultiplier=seq(2,6,0.5)
+ )
-----------------------  
Choosing betamultiplier  2 

 Number of remaining variables 4 
Testing variable contributions... 
Calculating average AUC values from 10 maxent models... 
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
Error: Unable to access jarfile C:/.../maxent.jar
Warning in system(paste("java -jar", maxent, "-o", outdir, "-j", gridfolder,  :
  running command 'java -jar C:/.../maxent.jar -o OutputDirectory -j BioORACLEVariables -s OutputDirectory/Occurrencedata.csv_VariableSubset.csv -e OutputDirectory/Backgrounddata.csv_VariableSubset.csv plots=false writeplotdata=false visible=false autorun=true randomseed=true writebackgroundpredictions=false replicates=10 replicatetype=subsample randomtestpoints=50 redoifexists writemess=false writeclampgrid=false askoverwrite=false pictures=false outputgrids=false -b 2 nolinear noquadratic noproduct nothreshold noautofeature >/dev/null' had status 1
Warning in file(file, "rt") :
  cannot open file 'OutputDirectory/maxentResults.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: VariableSelection -> MaxentAUC -> read.csv -> read.table -> file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/12s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘OutputDirectory’
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/MaxentVariableSelection.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 0:55.88, 45.81 + 8.52