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CHECK report for CausalR on merida2

This page was generated on 2019-04-09 13:31:38 -0400 (Tue, 09 Apr 2019).

Package 214/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.15.1
Glyn Bradley , Steven Barrett
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CausalR
Branch: master
Last Commit: c2ba57a
Last Changed Date: 2019-01-04 13:21:59 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: CausalR
Version: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2019-04-08 23:41:32 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:42:11 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 39.5 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CausalR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.1’
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘CausalR’ ...
** 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
* DONE (CausalR)

Tests output

CausalR.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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/RtmpH7ZI4K-492908415/corExplainedNodes-file11e0375536711.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-492908415/corExplainedNodes-file11e0375536711_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/RtmpH7ZI4K-362452882/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-362452882/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/RtmpH7ZI4K-150733447/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-150733447/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/RtmpH7ZI4K-150733447/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-150733447/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/RtmpH7ZI4K-150733447/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-150733447/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/RtmpH7ZI4K/corExplainedNodes-file11e0362bfb262.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/corExplainedNodes-file11e0362bfb262_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: /tmp/RtmpH7ZI4K/incorExplainedNodes-file11e0362bfb262.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/incorExplainedNodes-file11e0362bfb262_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/RtmpH7ZI4K/ambExplainedNodes-file11e0362bfb262.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/ambExplainedNodes-file11e0362bfb262_anno.txt
ambExplainedNodes 

Writing sif file to: /tmp/RtmpH7ZI4K/corExplainedNodes-file11e0317587294.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/corExplainedNodes-file11e0317587294_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/RtmpH7ZI4K/incorExplainedNodes-file11e0317587294.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/incorExplainedNodes-file11e0317587294_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/RtmpH7ZI4K/ambExplainedNodes-file11e0317587294.sif
Writing annotation file to: /tmp/RtmpH7ZI4K/ambExplainedNodes-file11e0317587294_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: /tmp/RtmpH7ZI4K-663890953/corExplainedNodes-file11e032fca5e85.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-663890953/corExplainedNodes-file11e032fca5e85_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/RtmpH7ZI4K-478148849/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-478148849/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/RtmpH7ZI4K-735343243/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-735343243/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/RtmpH7ZI4K-735343243/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-735343243/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/RtmpH7ZI4K-735343243/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpH7ZI4K-735343243/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5


RUNIT TEST PROTOCOL -- Mon Apr  8 23:42:05 2019 
*********************************************** 
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 
  3.183   0.841   3.684 

Example timings

CausalR.Rcheck/CausalR-Ex.timings

nameusersystemelapsed
AnalysePredictionsList0.0470.0040.052
CalculateEnrichmentPValue0.0030.0000.004
CalculateSignificance0.0790.0020.082
CalculateSignificanceUsingCubicAlgorithm0.0710.0020.073
CalculateSignificanceUsingCubicAlgorithm1b0.0400.0010.040
CalculateSignificanceUsingQuarticAlgorithm0.0740.0010.075
CompareHypothesis0.0110.0010.012
CreateCCG0.0070.0010.007
CreateCG0.0070.0010.007
GetNodeName0.0120.0000.012
GetNumberOfPositiveAndNegativeEntries0.0020.0000.003
GetShortestPathsFromCCG0.0190.0010.019
MakePredictions0.0130.0000.013
MakePredictionsFromCCG0.0150.0000.015
MakePredictionsFromCG0.0790.0020.080
PlotGraphWithNodeNames0.0970.0020.100
RankTheHypotheses0.1380.0490.146
ReadExperimentalData0.0340.0060.041
ScoreHypothesis0.0060.0010.007
WriteAllExplainedNodesToSifFile0.1830.0870.205
WriteExplainedNodesToSifFile0.0940.0010.096
runSCANR0.7990.1270.917