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CHECK report for CausalR on machv2

This page was generated on 2020-10-17 11:58:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CausalR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 237/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.20.0
Glyn Bradley , Steven Barrett
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CausalR
Branch: RELEASE_3_11
Last Commit: 55a37b2
Last Changed Date: 2020-04-27 14:49:15 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CausalR
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CausalR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CausalR_1.20.0.tar.gz
StartedAt: 2020-10-16 23:25:14 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:26:00 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 46.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CausalR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CausalR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CausalR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.20.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CausalR.Rcheck/00check.log’
for details.



Installation output

CausalR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CausalR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CausalR’ ...
** 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)

Tests output

CausalR.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
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/Rtmpiaww6s-6503875/corExplainedNodes-file17c0d2bbae750.sif
Writing annotation file to: /tmp/Rtmpiaww6s-6503875/corExplainedNodes-file17c0d2bbae750_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmpiaww6s-425169317/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-425169317/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/Rtmpiaww6s-464615424/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-464615424/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/Rtmpiaww6s-464615424/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-464615424/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmpiaww6s-464615424/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-464615424/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/Rtmpiaww6s/corExplainedNodes-file17c0d2012c090.sif
Writing annotation file to: /tmp/Rtmpiaww6s/corExplainedNodes-file17c0d2012c090_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: /tmp/Rtmpiaww6s/incorExplainedNodes-file17c0d2012c090.sif
Writing annotation file to: /tmp/Rtmpiaww6s/incorExplainedNodes-file17c0d2012c090_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmpiaww6s/ambExplainedNodes-file17c0d2012c090.sif
Writing annotation file to: /tmp/Rtmpiaww6s/ambExplainedNodes-file17c0d2012c090_anno.txt
ambExplainedNodes 

Writing sif file to: /tmp/Rtmpiaww6s/corExplainedNodes-file17c0d2f203e63.sif
Writing annotation file to: /tmp/Rtmpiaww6s/corExplainedNodes-file17c0d2f203e63_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmpiaww6s/incorExplainedNodes-file17c0d2f203e63.sif
Writing annotation file to: /tmp/Rtmpiaww6s/incorExplainedNodes-file17c0d2f203e63_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmpiaww6s/ambExplainedNodes-file17c0d2f203e63.sif
Writing annotation file to: /tmp/Rtmpiaww6s/ambExplainedNodes-file17c0d2f203e63_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: /tmp/Rtmpiaww6s-215379276/corExplainedNodes-file17c0d6ddfedc0.sif
Writing annotation file to: /tmp/Rtmpiaww6s-215379276/corExplainedNodes-file17c0d6ddfedc0_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmpiaww6s-395703994/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-395703994/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/Rtmpiaww6s-22517137/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-22517137/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/Rtmpiaww6s-22517137/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-22517137/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmpiaww6s-22517137/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmpiaww6s-22517137/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5


RUNIT TEST PROTOCOL -- Fri Oct 16 23:25:50 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 
  2.942   0.632   3.457 

Example timings

CausalR.Rcheck/CausalR-Ex.timings

nameusersystemelapsed
AnalysePredictionsList0.0460.0060.052
CalculateEnrichmentPValue0.0030.0010.004
CalculateSignificance0.0800.0020.083
CalculateSignificanceUsingCubicAlgorithm0.0880.0010.090
CalculateSignificanceUsingCubicAlgorithm1b0.0780.0010.078
CalculateSignificanceUsingQuarticAlgorithm0.0890.0010.090
CompareHypothesis0.0120.0010.014
CreateCCG0.0110.0010.012
CreateCG0.0120.0010.013
GetNodeName0.0120.0000.012
GetNumberOfPositiveAndNegativeEntries0.0010.0000.003
GetShortestPathsFromCCG0.0160.0010.016
MakePredictions0.0130.0010.014
MakePredictionsFromCCG0.0120.0010.013
MakePredictionsFromCG0.0710.0020.072
PlotGraphWithNodeNames0.1070.0030.110
RankTheHypotheses0.1160.0520.136
ReadExperimentalData0.0230.0040.028
ScoreHypothesis0.0050.0010.007
WriteAllExplainedNodesToSifFile0.2140.1520.240
WriteExplainedNodesToSifFile0.0730.0030.076
runSCANR0.6770.1140.723