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This page was generated on 2022-06-27 11:05:24 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
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CHECK results for MOGAMUN on nebbiolo2


To the developers/maintainers of the MOGAMUN package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOGAMUN.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1210/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOGAMUN 1.7.0  (landing page)
Elva-María Novoa-del-Toro
Snapshot Date: 2022-06-26 14:00:03 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/MOGAMUN
git_branch: master
git_last_commit: 51c08bd
git_last_commit_date: 2022-04-26 12:09:50 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MOGAMUN
Version: 1.7.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings MOGAMUN_1.7.0.tar.gz
StartedAt: 2022-06-26 20:40:09 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 20:40:59 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 49.7 seconds
RetCode: 0
Status:   OK  
CheckDir: MOGAMUN.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MOGAMUN.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings MOGAMUN_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MOGAMUN.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.7.0’
* 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


Installation output

MOGAMUN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MOGAMUN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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)

Tests output

MOGAMUN.Rcheck/tests/unitTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 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: 0.025 0 0.025
Error in is.igraph(LoadedData$Multiplex[[i]]) : 
  could not find function "is.igraph"
In addition: Warning messages:
1: In LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <=  :
  'length(x) = 1000 > 1' in coercion to 'logical(1)'
2: In LoadedData$GenesWithNodesScores$nodescore >= 0 && LoadedData$GenesWithNodesScores$nodescore <=  :
  'length(x) = 1000 > 1' in coercion to 'logical(1)'
 done successfully.



Executing test function test.mogamun_postprocess  ... [1] "Attempt to add a new neighbor FAILED. Rolling back mutation"
[1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2022-06-26 20:40:55"
Timing stopped at: 0.843 0.043 0.887
Error in checkIdentical(RealOutput, ExpectedOutput) : FALSE 
 
In addition: Warning message:
In dir.create(ResultsPath, recursive = TRUE) :
  '/home/biocbuild/bbs-3.16-bioc/R/library/MOGAMUN/SampleResults//Experiment_2022-06-26' already exists
 done successfully.



Executing test function test.mogamun_run  ... [1] "Keeping similar individuals. Inf crowding distance."
     Individual AverageNodesScore  Density Rank CrowdingDistance
2  157, 159....         0.4661866 83.67462    1              Inf
12 103, 157....         0.5169334 22.33047    1              Inf
[1] "Run 1. Gen. 1 completed"
[1] "FINISH TIME, RUN 1: 2022-06-26 20:40:56"
Timing stopped at: 0.695 0.001 0.696
Error in checkEquals(length(list.files(ResDirAll)), 2) : 
  Mean relative difference: 0.75

In addition: Warning message:
In dir.create(ResultsPath, recursive = TRUE) :
  '/home/biocbuild/bbs-3.16-bioc/R/library/MOGAMUN/SampleResults//Experiment_2022-06-26' already exists
 done successfully.

RUNIT TEST PROTOCOL -- Sun Jun 26 20:40:56 2022 
*********************************************** 
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-3.16-bioc/R/library/MOGAMUN/tests/ 
--------------------------- 
Test file: /home/biocbuild/bbs-3.16-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 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 
  3.118   0.154   3.255 

Example timings

MOGAMUN.Rcheck/MOGAMUN-Ex.timings

nameusersystemelapsed
mogamun_init0.0010.0010.000
mogamun_load_data0.0280.0000.028
mogamun_postprocess0.8960.0670.964
mogamun_run0.8000.0010.800