Glyn Bradley
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CausalR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 4a392e7 |
| git_last_commit_date: 2021-05-19 12:13:52 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CausalR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CausalR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 247/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CausalR 1.24.0 (landing page) Glyn Bradley
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CausalR |
| Version: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2021-10-14 17:06:28 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:07:11 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 43.6 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CausalR.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.24.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
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/RtmpIfEGQv-854842625/corExplainedNodes-filee24d60c592c2.sif
Writing annotation file to: /tmp/RtmpIfEGQv-854842625/corExplainedNodes-filee24d60c592c2_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIfEGQv-622244710/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-622244710/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/RtmpIfEGQv-953669016/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-953669016/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/RtmpIfEGQv-953669016/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-953669016/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIfEGQv-953669016/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-953669016/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/RtmpIfEGQv/corExplainedNodes-filee24d37e0c9a9.sif
Writing annotation file to: /tmp/RtmpIfEGQv/corExplainedNodes-filee24d37e0c9a9_anno.txt
corExplainedNodes
Node0 Activates Node1
Writing sif file to: /tmp/RtmpIfEGQv/incorExplainedNodes-filee24d37e0c9a9.sif
Writing annotation file to: /tmp/RtmpIfEGQv/incorExplainedNodes-filee24d37e0c9a9_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIfEGQv/ambExplainedNodes-filee24d37e0c9a9.sif
Writing annotation file to: /tmp/RtmpIfEGQv/ambExplainedNodes-filee24d37e0c9a9_anno.txt
ambExplainedNodes
Writing sif file to: /tmp/RtmpIfEGQv/corExplainedNodes-filee24d6d792e8.sif
Writing annotation file to: /tmp/RtmpIfEGQv/corExplainedNodes-filee24d6d792e8_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIfEGQv/incorExplainedNodes-filee24d6d792e8.sif
Writing annotation file to: /tmp/RtmpIfEGQv/incorExplainedNodes-filee24d6d792e8_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIfEGQv/ambExplainedNodes-filee24d6d792e8.sif
Writing annotation file to: /tmp/RtmpIfEGQv/ambExplainedNodes-filee24d6d792e8_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
Writing sif file to: /tmp/RtmpIfEGQv-739871712/corExplainedNodes-filee24d32edc0da.sif
Writing annotation file to: /tmp/RtmpIfEGQv-739871712/corExplainedNodes-filee24d32edc0da_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIfEGQv-933352528/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-933352528/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/RtmpIfEGQv-570203739/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-570203739/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/RtmpIfEGQv-570203739/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-570203739/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIfEGQv-570203739/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIfEGQv-570203739/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
RUNIT TEST PROTOCOL -- Thu Oct 14 17:07:03 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
2.798 0.612 3.310
CausalR.Rcheck/CausalR-Ex.timings
| name | user | system | elapsed | |
| AnalysePredictionsList | 0.038 | 0.004 | 0.042 | |
| CalculateEnrichmentPValue | 0.003 | 0.000 | 0.004 | |
| CalculateSignificance | 0.066 | 0.003 | 0.070 | |
| CalculateSignificanceUsingCubicAlgorithm | 0.083 | 0.001 | 0.084 | |
| CalculateSignificanceUsingCubicAlgorithm1b | 0.073 | 0.001 | 0.074 | |
| CalculateSignificanceUsingQuarticAlgorithm | 0.080 | 0.001 | 0.082 | |
| CompareHypothesis | 0.012 | 0.001 | 0.012 | |
| CreateCCG | 0.012 | 0.001 | 0.013 | |
| CreateCG | 0.008 | 0.001 | 0.010 | |
| GetNodeName | 0.012 | 0.001 | 0.013 | |
| GetNumberOfPositiveAndNegativeEntries | 0.002 | 0.000 | 0.003 | |
| GetShortestPathsFromCCG | 0.016 | 0.001 | 0.017 | |
| MakePredictions | 0.021 | 0.000 | 0.022 | |
| MakePredictionsFromCCG | 0.014 | 0.001 | 0.014 | |
| MakePredictionsFromCG | 0.051 | 0.003 | 0.053 | |
| PlotGraphWithNodeNames | 0.092 | 0.003 | 0.095 | |
| RankTheHypotheses | 0.108 | 0.049 | 0.121 | |
| ReadExperimentalData | 0.020 | 0.004 | 0.023 | |
| ScoreHypothesis | 0.005 | 0.002 | 0.006 | |
| WriteAllExplainedNodesToSifFile | 0.197 | 0.134 | 0.222 | |
| WriteExplainedNodesToSifFile | 0.049 | 0.002 | 0.051 | |
| runSCANR | 0.557 | 0.102 | 0.598 | |