Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:06:51 -0400 (Wed, 16 Oct 2019).
Package 217/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
CausalR 1.16.0 Glyn Bradley
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: CausalR |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CausalR_1.16.0.tar.gz |
StartedAt: 2019-10-16 00:18:46 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 00:19:20 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 33.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CausalR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CausalR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CausalR.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’ * 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 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/CausalR.Rcheck/00check.log’ for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CausalR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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/RtmpKzYOao-903801552/corExplainedNodes-file24d760490a84.sif Writing annotation file to: /tmp/RtmpKzYOao-903801552/corExplainedNodes-file24d760490a84_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpKzYOao-606847199/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-606847199/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/RtmpKzYOao-573221759/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-573221759/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/RtmpKzYOao-573221759/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-573221759/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpKzYOao-573221759/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-573221759/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/RtmpKzYOao/corExplainedNodes-file24d733ccac60.sif Writing annotation file to: /tmp/RtmpKzYOao/corExplainedNodes-file24d733ccac60_anno.txt corExplainedNodes Node0 Activates Node1 Writing sif file to: /tmp/RtmpKzYOao/incorExplainedNodes-file24d733ccac60.sif Writing annotation file to: /tmp/RtmpKzYOao/incorExplainedNodes-file24d733ccac60_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpKzYOao/ambExplainedNodes-file24d733ccac60.sif Writing annotation file to: /tmp/RtmpKzYOao/ambExplainedNodes-file24d733ccac60_anno.txt ambExplainedNodes Writing sif file to: /tmp/RtmpKzYOao/corExplainedNodes-file24d71333519a.sif Writing annotation file to: /tmp/RtmpKzYOao/corExplainedNodes-file24d71333519a_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpKzYOao/incorExplainedNodes-file24d71333519a.sif Writing annotation file to: /tmp/RtmpKzYOao/incorExplainedNodes-file24d71333519a_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpKzYOao/ambExplainedNodes-file24d71333519a.sif Writing annotation file to: /tmp/RtmpKzYOao/ambExplainedNodes-file24d71333519a_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 Writing sif file to: /tmp/RtmpKzYOao-426425307/corExplainedNodes-file24d724199484.sif Writing annotation file to: /tmp/RtmpKzYOao-426425307/corExplainedNodes-file24d724199484_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: /tmp/RtmpKzYOao-217374481/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-217374481/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/RtmpKzYOao-244221857/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-244221857/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/RtmpKzYOao-244221857/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-244221857/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: /tmp/RtmpKzYOao-244221857/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: /tmp/RtmpKzYOao-244221857/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 RUNIT TEST PROTOCOL -- Wed Oct 16 00:19:15 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 2.851 0.517 3.528
CausalR.Rcheck/CausalR-Ex.timings
name | user | system | elapsed | |
AnalysePredictionsList | 0.032 | 0.004 | 0.047 | |
CalculateEnrichmentPValue | 0.003 | 0.000 | 0.003 | |
CalculateSignificance | 0.068 | 0.000 | 0.068 | |
CalculateSignificanceUsingCubicAlgorithm | 0.072 | 0.000 | 0.072 | |
CalculateSignificanceUsingCubicAlgorithm1b | 0.056 | 0.000 | 0.056 | |
CalculateSignificanceUsingQuarticAlgorithm | 0.063 | 0.004 | 0.068 | |
CompareHypothesis | 0.01 | 0.00 | 0.01 | |
CreateCCG | 0.006 | 0.004 | 0.009 | |
CreateCG | 0.007 | 0.000 | 0.008 | |
GetNodeName | 0.013 | 0.000 | 0.012 | |
GetNumberOfPositiveAndNegativeEntries | 0.002 | 0.000 | 0.002 | |
GetShortestPathsFromCCG | 0.011 | 0.000 | 0.011 | |
MakePredictions | 0.016 | 0.000 | 0.016 | |
MakePredictionsFromCCG | 0.012 | 0.000 | 0.011 | |
MakePredictionsFromCG | 0.069 | 0.000 | 0.068 | |
PlotGraphWithNodeNames | 0.09 | 0.00 | 0.09 | |
RankTheHypotheses | 0.094 | 0.032 | 0.099 | |
ReadExperimentalData | 0.019 | 0.008 | 0.027 | |
ScoreHypothesis | 0.005 | 0.000 | 0.004 | |
WriteAllExplainedNodesToSifFile | 0.129 | 0.040 | 0.122 | |
WriteExplainedNodesToSifFile | 0.067 | 0.003 | 0.074 | |
runSCANR | 0.659 | 0.047 | 0.666 | |