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This page was generated on 2021-05-06 12:34:29 -0400 (Thu, 06 May 2021).
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 240/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CausalR 1.22.0 (landing page) Glyn Bradley
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CausalR |
Version: 1.22.0 |
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_1.22.0.tar.gz |
StartedAt: 2021-05-05 23:59:18 -0400 (Wed, 05 May 2021) |
EndedAt: 2021-05-05 23:59:58 -0400 (Wed, 05 May 2021) |
EllapsedTime: 40.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CausalR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/CausalR.Rcheck’ * using R version 4.0.5 (2021-03-31) * 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 ‘1.22.0’ * 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-3.12-bioc/meat/CausalR.Rcheck/00check.log’ for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
CausalR.Rcheck/tests/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 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/RtmpFzT9ox-84729351/corExplainedNodes-file9a48342e7a7d.sif Writing annotation file to: /tmp/RtmpFzT9ox-84729351/corExplainedNodes-file9a48342e7a7d_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpFzT9ox-582418742/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-582418742/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/RtmpFzT9ox-640279198/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-640279198/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/RtmpFzT9ox-640279198/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-640279198/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpFzT9ox-640279198/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-640279198/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/RtmpFzT9ox/corExplainedNodes-file9a48c7a8cbd.sif Writing annotation file to: /tmp/RtmpFzT9ox/corExplainedNodes-file9a48c7a8cbd_anno.txt corExplainedNodes Node0 Activates Node1 Writing sif file to: /tmp/RtmpFzT9ox/incorExplainedNodes-file9a48c7a8cbd.sif Writing annotation file to: /tmp/RtmpFzT9ox/incorExplainedNodes-file9a48c7a8cbd_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpFzT9ox/ambExplainedNodes-file9a48c7a8cbd.sif Writing annotation file to: /tmp/RtmpFzT9ox/ambExplainedNodes-file9a48c7a8cbd_anno.txt ambExplainedNodes Writing sif file to: /tmp/RtmpFzT9ox/corExplainedNodes-file9a4841add2b1.sif Writing annotation file to: /tmp/RtmpFzT9ox/corExplainedNodes-file9a4841add2b1_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpFzT9ox/incorExplainedNodes-file9a4841add2b1.sif Writing annotation file to: /tmp/RtmpFzT9ox/incorExplainedNodes-file9a4841add2b1_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpFzT9ox/ambExplainedNodes-file9a4841add2b1.sif Writing annotation file to: /tmp/RtmpFzT9ox/ambExplainedNodes-file9a4841add2b1_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 Writing sif file to: /tmp/RtmpFzT9ox-732166111/corExplainedNodes-file9a487ae38426.sif Writing annotation file to: /tmp/RtmpFzT9ox-732166111/corExplainedNodes-file9a487ae38426_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpFzT9ox-32653365/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-32653365/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/RtmpFzT9ox-551139942/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-551139942/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/RtmpFzT9ox-551139942/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-551139942/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpFzT9ox-551139942/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpFzT9ox-551139942/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 RUNIT TEST PROTOCOL -- Wed May 5 23:59:49 2021 *********************************************** 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 2.750 0.583 3.124
CausalR.Rcheck/CausalR-Ex.timings
name | user | system | elapsed | |
AnalysePredictionsList | 0.042 | 0.005 | 0.047 | |
CalculateEnrichmentPValue | 0.002 | 0.000 | 0.003 | |
CalculateSignificance | 0.078 | 0.002 | 0.080 | |
CalculateSignificanceUsingCubicAlgorithm | 0.054 | 0.000 | 0.054 | |
CalculateSignificanceUsingCubicAlgorithm1b | 0.063 | 0.001 | 0.063 | |
CalculateSignificanceUsingQuarticAlgorithm | 0.078 | 0.001 | 0.080 | |
CompareHypothesis | 0.012 | 0.001 | 0.014 | |
CreateCCG | 0.010 | 0.001 | 0.011 | |
CreateCG | 0.009 | 0.001 | 0.010 | |
GetNodeName | 0.014 | 0.000 | 0.014 | |
GetNumberOfPositiveAndNegativeEntries | 0.002 | 0.001 | 0.003 | |
GetShortestPathsFromCCG | 0.014 | 0.001 | 0.015 | |
MakePredictions | 0.014 | 0.000 | 0.015 | |
MakePredictionsFromCCG | 0.012 | 0.001 | 0.013 | |
MakePredictionsFromCG | 0.058 | 0.002 | 0.059 | |
PlotGraphWithNodeNames | 0.100 | 0.003 | 0.104 | |
RankTheHypotheses | 0.125 | 0.063 | 0.138 | |
ReadExperimentalData | 0.024 | 0.004 | 0.029 | |
ScoreHypothesis | 0.006 | 0.002 | 0.007 | |
WriteAllExplainedNodesToSifFile | 0.146 | 0.096 | 0.176 | |
WriteExplainedNodesToSifFile | 0.059 | 0.003 | 0.061 | |
runSCANR | 0.597 | 0.156 | 0.643 | |