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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MOGAMUN_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MOGAMUN.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOGAMUN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOGAMUN’ version ‘1.0.1’
* 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 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 R 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 in ‘inst/doc’ ... 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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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MOGAMUN
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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: 0.028 0 0.031
Error in is.igraph(LoadedData$Multiplex[[i]]) : 
  could not find function "is.igraph"
 done successfully.



Executing test function test.mogamun_postprocess  ... [1] "Keeping similar individuals. Inf crowding distance."
     Individual AverageNodesScore  Density Rank CrowdingDistance
16 57, 106,....         0.4836834 22.37090    1              Inf
17 52, 53, ....         0.4412627 48.02097    1              Inf
[1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2021-05-06 03:40:41"
Timing stopped at: 2.148 0.008 2.174
Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE 
 
In addition: Warning messages:
1: In dir.create(ResultsPath, recursive = TRUE) :
  '/home/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/SampleResults//Experiment_2021-05-06' already exists
2: In sink(NULL, type = "output") : no sink to remove
 done successfully.



Executing test function test.mogamun_run  ... [1] "Keeping similar individuals. Inf crowding distance."
     Individual AverageNodesScore  Density Rank CrowdingDistance
16 57, 106,....         0.4836834 22.37090    1              Inf
17 52, 53, ....         0.4412627 48.02097    1              Inf
[1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2021-05-06 03:40:43"
Timing stopped at: 1.976 0.024 2.007
Error in checkEquals(length(list.files(ResDirAll)), 2) : 
  Mean relative difference: 0.75

In addition: Warning messages:
1: In dir.create(ResultsPath, recursive = TRUE) :
  '/home/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/SampleResults//Experiment_2021-05-06' already exists
2: In sink(NULL, type = "output") : no sink to remove
 done successfully.

RUNIT TEST PROTOCOL -- Thu May  6 03:40:43 2021 
*********************************************** 
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 is.igraph(LoadedData$Multiplex[[i]]) : 
  could not find function "is.igraph"
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: 
/home/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/tests/ 
--------------------------- 
Test file: /home/biocbuild/bbs-3.12-bioc/R/library/MOGAMUN/tests//test.mogamun.R 
test.mogamun_init: (13 checks) ... OK (0 seconds)
test.mogamun_load_data: ERROR !! 
Error in is.igraph(LoadedData$Multiplex[[i]]) : 
  could not find function "is.igraph"
test.mogamun_postprocess: FAILURE !! (check number 6)
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 
  5.224   0.088   5.335