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CHECK report for CausalR on tokay1

This page was generated on 2020-04-15 12:25:02 -0400 (Wed, 15 Apr 2020).

Package 231/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.18.0
Glyn Bradley , Steven Barrett
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CausalR
Branch: RELEASE_3_10
Last Commit: f2d6c69
Last Changed Date: 2019-10-29 13:09:19 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CausalR
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CausalR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CausalR_1.18.0.tar.gz
StartedAt: 2020-04-15 01:50:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:51:47 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 87.8 seconds
RetCode: 0
Status:  OK  
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CausalR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings CausalR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/CausalR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CausalR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CausalR' version '1.18.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/CausalR.Rcheck/00check.log'
for details.

Installation output

CausalR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/CausalR_1.18.0.tar.gz && rm -rf CausalR.buildbin-libdir && mkdir CausalR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CausalR.buildbin-libdir CausalR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL CausalR_1.18.0.zip && rm CausalR_1.18.0.tar.gz CausalR_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  192k  100  192k    0     0  4747k      0 --:--:-- --:--:-- --:--:-- 5194k

install for i386

* installing *source* package 'CausalR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CausalR'
    finding HTML links ... done
    AddIDsToVertices                        html  
    AddWeightsToEdges                       html  
    AnalyseExperimentalData                 html  
    AnalysePredictionsList                  html  
    CalculateEnrichmentPValue               html  
    CalculateSignificance                   html  
    CalculateSignificanceUsingCubicAlgorithm
                                            html  
    CalculateSignificanceUsingCubicAlgorithm1b
                                            html  
    CalculateSignificanceUsingQuarticAlgorithm
                                            html  
    CalculateTotalWeightForAllContingencyTables
                                            html  
    CalculateWeightGivenValuesInThreeByThreeContingencyTable
                                            html  
    CausalR-package                         html  
    CheckPossibleValuesAreValid             html  
    CheckRowAndColumnSumValuesAreValid      html  
    CompareHypothesis                       html  
    ComputeFinalDistribution                html  
    ComputePValueFromDistributionTable      html  
    CreateCCG                               html  
    CreateCG                                html  
    CreateNetworkFromTable                  html  
    DetermineInteractionTypeOfPath          html  
    FindApproximateValuesThatWillMaximiseDValue
                                            html  
    FindIdsOfConnectedNodesInSubgraph       html  
    FindMaximumDValue                       html  
    GetAllPossibleRoundingCombinations      html  
    GetApproximateMaximumDValueFromThreeByTwoContingencyTable
                                            html  
    GetApproximateMaximumDValueFromTwoByTwoContingencyTable
                                            html  
    GetCombinationsOfCorrectandIncorrectPredictions
                                            html  
    GetExplainedNodesOfCCG                  html  
    GetInteractionInformation               html  
    GetMatrixOfCausalRelationships          html  
    GetMaxDValueForAFamily                  html  
    GetMaxDValueForAThreeByTwoFamily        html  
    GetMaximumDValueFromTwoByTwoContingencyTable
                                            html  
    GetNodeID                               html  
    GetNodeName                             html  
    GetNumberOfPositiveAndNegativeEntries   html  
    GetPathsInSifFormat                     html  
    GetRegulatedNodes                       html  
    GetRowAndColumnSumValues                html  
    GetScoreForNumbersOfCorrectandIncorrectPredictions
                                            html  
    GetScoresForSingleNode                  html  
    GetScoresWeightsMatrix                  html  
    GetScoresWeightsMatrixByCubicAlg        html  
    GetSetOfDifferentiallyExpressedGenes    html  
    GetSetOfSignificantPredictions          html  
    GetShortestPathsFromCCG                 html  
    GetWeightForNumbersOfCorrectandIncorrectPredictions
                                            html  
    GetWeightsAboveHypothesisScoreAndTotalWeights
                                            html  
    GetWeightsAboveHypothesisScoreForAThreeByTwoTable
                                            html  
    GetWeightsFromInteractionInformation    html  
    MakePredictions                         html  
    MakePredictionsFromCCG                  html  
    MakePredictionsFromCG                   html  
    OrderHypotheses                         html  
    PlotGraphWithNodeNames                  html  
    PopulateTheThreeByThreeContingencyTable
                                            html  
    PopulateTwoByTwoContingencyTable        html  
    ProcessExperimentalData                 html  
    RankTheHypotheses                       html  
    ReadExperimentalData                    html  
    ReadSifFileToTable                      html  
    RemoveIDsNotInExperimentalData          html  
    ScoreHypothesis                         html  
    ValidateFormatOfDataTable               html  
    ValidateFormatOfTable                   html  
    WriteAllExplainedNodesToSifFile         html  
    WriteExplainedNodesToSifFile            html  
    runRankHypothesis                       html  
    runSCANR                                html  
** 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

install for x64

* installing *source* package 'CausalR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CausalR' as CausalR_1.18.0.zip
* DONE (CausalR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'CausalR' successfully unpacked and MD5 sums checked

Tests output

CausalR.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> # 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 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
[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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-826587068/corExplainedNodes-file21143d883c37.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-826587068/corExplainedNodes-file21143d883c37_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-81214582/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-81214582/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-128087809/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/corExplainedNodes-file21142472437e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/corExplainedNodes-file21142472437e_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/incorExplainedNodes-file21142472437e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/incorExplainedNodes-file21142472437e_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/ambExplainedNodes-file21142472437e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/ambExplainedNodes-file21142472437e_anno.txt
ambExplainedNodes 

Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/corExplainedNodes-file2114d42604e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/corExplainedNodes-file2114d42604e_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/incorExplainedNodes-file2114d42604e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/incorExplainedNodes-file2114d42604e_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/ambExplainedNodes-file2114d42604e.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA/ambExplainedNodes-file2114d42604e_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-327746466/corExplainedNodes-file211433892eba.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-327746466/corExplainedNodes-file211433892eba_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-675801537/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-675801537/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpKKoWuA-459547835/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5


RUNIT TEST PROTOCOL -- Wed Apr 15 01:51:28 2020 
*********************************************** 
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 
   1.98    0.18   12.73

CausalR.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

> # 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 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 2 
Number of Nodes to analyse: 2 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 1 
Number of Nodes to analyse: 1 
Parallel processing. Number of cores: 2 
Number of Nodes to analyse: 3 
Number of Nodes to analyse: 3 
Parallel processing. Number of cores: 2 
[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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-118634192/corExplainedNodes-file17ac6143975.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-118634192/corExplainedNodes-file17ac6143975_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-387548819/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-387548819/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-756860595/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/corExplainedNodes-file17ac835266.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/corExplainedNodes-file17ac835266_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/incorExplainedNodes-file17ac835266.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/incorExplainedNodes-file17ac835266_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/ambExplainedNodes-file17ac835266.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/ambExplainedNodes-file17ac835266_anno.txt
ambExplainedNodes 

Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/corExplainedNodes-file17ac450b204b.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/corExplainedNodes-file17ac450b204b_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/incorExplainedNodes-file17ac450b204b.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/incorExplainedNodes-file17ac450b204b_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/ambExplainedNodes-file17ac450b204b.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ/ambExplainedNodes-file17ac450b204b_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-6435783/corExplainedNodes-file17ac595d337.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-6435783/corExplainedNodes-file17ac595d337_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-662963291/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-662963291/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/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: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpwj6yyQ-427132126/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5


RUNIT TEST PROTOCOL -- Wed Apr 15 01:51:41 2020 
*********************************************** 
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 
   2.59    0.20   12.81

Example timings

CausalR.Rcheck/examples_i386/CausalR-Ex.timings

nameusersystemelapsed
AnalysePredictionsList0.060.000.27
CalculateEnrichmentPValue000
CalculateSignificance0.080.000.08
CalculateSignificanceUsingCubicAlgorithm0.080.000.08
CalculateSignificanceUsingCubicAlgorithm1b0.050.000.04
CalculateSignificanceUsingQuarticAlgorithm0.080.000.08
CompareHypothesis0.000.000.08
CreateCCG0.000.020.02
CreateCG000
GetNodeName0.010.000.01
GetNumberOfPositiveAndNegativeEntries000
GetShortestPathsFromCCG0.000.010.02
MakePredictions0.020.000.01
MakePredictionsFromCCG0.010.000.02
MakePredictionsFromCG0.070.000.06
PlotGraphWithNodeNames0.120.000.13
RankTheHypotheses0.130.020.61
ReadExperimentalData000
ScoreHypothesis000
WriteAllExplainedNodesToSifFile0.060.001.05
WriteExplainedNodesToSifFile0.040.010.06
runSCANR0.470.023.27

CausalR.Rcheck/examples_x64/CausalR-Ex.timings

nameusersystemelapsed
AnalysePredictionsList0.030.020.05
CalculateEnrichmentPValue000
CalculateSignificance0.080.000.08
CalculateSignificanceUsingCubicAlgorithm0.080.000.08
CalculateSignificanceUsingCubicAlgorithm1b0.060.010.08
CalculateSignificanceUsingQuarticAlgorithm0.080.000.07
CompareHypothesis0.000.000.04
CreateCCG0.020.000.06
CreateCG0.010.000.01
GetNodeName0.030.000.05
GetNumberOfPositiveAndNegativeEntries000
GetShortestPathsFromCCG0.020.000.03
MakePredictions0.000.000.03
MakePredictionsFromCCG0.020.000.01
MakePredictionsFromCG0.060.000.19
PlotGraphWithNodeNames0.130.000.13
RankTheHypotheses0.090.000.95
ReadExperimentalData0.030.000.03
ScoreHypothesis000
WriteAllExplainedNodesToSifFile0.060.021.44
WriteExplainedNodesToSifFile0.070.000.06
runSCANR0.480.011.78