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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CausalR_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CausalR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.40.0’
* 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 ‘CausalR’ 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 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 ... 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CausalR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CausalR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CausalR’ ...
** this is package ‘CausalR’ version ‘1.40.0’
** 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 (CausalR)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # Make sure that the igraph package has been loaded
> 
> library(igraph)

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> BiocGenerics:::testPackage("CausalR")
[1] "File read complete - read in 3 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
[1] "File read complete - read in 2 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
[1] "File read complete - read in 2 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
[1] "File read complete - read in 4 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
[1] "File read complete - read in 4 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
[1] "The values in the second column do not match what is expected. They should be (+)1, 0 or -1"
[1] "The experimental data read in didn't have two columns"
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
[1] "File read complete - read in 2 lines. Now constructing network"
[1] "Network has been created - now adding edge properties"
[1] "Added weights to edges"
Writing sif file to: /tmp/Rtmp0hrOAu-148082886/corExplainedNodes-file231ab71c4de109.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-148082886/corExplainedNodes-file231ab71c4de109_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-177771726/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-177771726/corExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-980911480/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-980911480/corExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-980911480/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-980911480/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp0hrOAu-980911480/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-980911480/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: /tmp/Rtmp0hrOAu/corExplainedNodes-file231ab77a0abb80.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/corExplainedNodes-file231ab77a0abb80_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: /tmp/Rtmp0hrOAu/incorExplainedNodes-file231ab77a0abb80.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/incorExplainedNodes-file231ab77a0abb80_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp0hrOAu/ambExplainedNodes-file231ab77a0abb80.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/ambExplainedNodes-file231ab77a0abb80_anno.txt
ambExplainedNodes 

Writing sif file to: /tmp/Rtmp0hrOAu/corExplainedNodes-file231ab72d9641d.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/corExplainedNodes-file231ab72d9641d_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu/incorExplainedNodes-file231ab72d9641d.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/incorExplainedNodes-file231ab72d9641d_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp0hrOAu/ambExplainedNodes-file231ab72d9641d.sif
Writing annotation file to: /tmp/Rtmp0hrOAu/ambExplainedNodes-file231ab72d9641d_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: /tmp/Rtmp0hrOAu-52234855/corExplainedNodes-file231ab77a766a46.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-52234855/corExplainedNodes-file231ab77a766a46_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-687449456/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-687449456/corExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-393356914/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-393356914/corExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp0hrOAu-393356914/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-393356914/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp0hrOAu-393356914/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp0hrOAu-393356914/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5


RUNIT TEST PROTOCOL -- Wed Oct 15 21:28:27 2025 
*********************************************** 
Number of test functions: 129 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CausalR RUnit Tests - 129 test functions, 0 errors, 0 failures
Number of test functions: 129 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In file(file, "rt") :
  cannot open file 'nonExistentFile.sif': No such file or directory
2: In file(file, "rt") :
  cannot open file 'nonExistentFile.sif': No such file or directory
> 
> proc.time()
   user  system elapsed 
  1.788   0.431   2.010