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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOGAMUN_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOGAMUN.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOGAMUN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOGAMUN’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MOGAMUN’ 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 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOGAMUN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MOGAMUN’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MOGAMUN)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Our package. Used for the test suite name
> pkgname <- c("MOGAMUN", "RUnit")
> 
> for (p in pkgname) {
+     require(p, quietly=TRUE, character.only=TRUE) || 
+     stop("package '", p, "' not found")
+ }
> 
> pkgname <- "MOGAMUN"
> 
> # Determine which files to load (have to start with test_ and end with .R)
> pattern <- "^test.*\\.R$"
> 
> # Which functions to run. Have to start with 'test.'
> testFunctionRegexp = "^test.+"
> 
> # Path to the unit tests folder in the package
> directory <- paste0(system.file("tests", package=pkgname), "/")
> if (.Platform$OS.type == "windows") { # windows needs the absolute file names
+     directory <- list.files(directory, pattern = pattern, full.names = TRUE)
+ } 
> 
> for (dir in directory) {
+     # Define RUnit test suite
+     suite <- defineTestSuite(name=paste(pkgname, "RUnit Tests"),
+                              dirs=dir,
+                              testFileRegexp=pattern,
+                              testFuncRegexp = testFunctionRegexp,
+                              rngKind="default",
+                              rngNormalKind="default")
+     
+     # Run tests
+     result <- runTestSuite(suite)
+     
+     # Display result tests on the console
+     printTextProtocol(result)
+     
+     # Write results in JUnit-like xml format
+     printJUnitProtocol(result, fileName="junit.xml")
+ }


Executing test function test.mogamun_init  ...  done successfully.



Executing test function test.mogamun_load_data  ... Timing stopped at: 0.012 0.002 0.012
Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <=  : 
  'length = 1000' in coercion to 'logical(1)'
 done successfully.



Executing test function test.mogamun_postprocess  ... [1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2024-10-27 20:26:23.074"
Timing stopped at: 0.32 0.013 0.328
Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE 
 
In addition: Warning message:
In dir.create(ResultsPath, recursive = TRUE) :
  '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/SampleResults//Experiment_2024-10-27' already exists
 done successfully.



Executing test function test.mogamun_run  ... [1] "Attempt to add a new neighbor FAILED. Rolling back mutation"
[1] "Keeping similar individuals. Inf crowding distance."
     Individual AverageNodesScore  Density Rank CrowdingDistance
15 52, 152,....         0.5063340 39.81506    1              Inf
20 52, 63, ....         0.4369761 61.36562    1              Inf
[1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2024-10-27 20:26:23.37664"
Timing stopped at: 0.267 0.007 0.274
Error in checkEquals(length(list.files(ResDirAll)), 2) : 
  Mean relative difference: 0.75

In addition: Warning message:
In dir.create(ResultsPath, recursive = TRUE) :
  '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/SampleResults//Experiment_2024-10-27' already exists
 done successfully.

RUNIT TEST PROTOCOL -- Sun Oct 27 20:26:23 2024 
*********************************************** 
Number of test functions: 4 
Number of errors: 1 
Number of failures: 2 

 
1 Test Suite : 
MOGAMUN RUnit Tests - 4 test functions, 1 error, 2 failures
ERROR in test.mogamun_load_data: Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <=  : 
  'length = 1000' in coercion to 'logical(1)'
FAILURE in test.mogamun_postprocess: Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE 
 
FAILURE in test.mogamun_run: Error in checkEquals(length(list.files(ResDirAll)), 2) : 
  Mean relative difference: 0.75




Details 
*************************** 
Test Suite: MOGAMUN RUnit Tests 
Test function regexp: ^test.+ 
Test file regexp: ^test.*\.R$ 
Involved directory: 
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/tests/ 
--------------------------- 
Test file: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/MOGAMUN/tests//test.mogamun.R 
test.mogamun_init: (13 checks) ... OK (0 seconds)
test.mogamun_load_data: ERROR !! 
Error in LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <=  : 
  'length = 1000' in coercion to 'logical(1)'
test.mogamun_postprocess: FAILURE !! (check number 2)
Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE 
 
test.mogamun_run: FAILURE !! (check number 2)
Error in checkEquals(length(list.files(ResDirAll)), 2) : 
  Mean relative difference: 0.75

> 
> 
> proc.time()
   user  system elapsed 
  1.120   0.061   1.175