Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:01 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CausalR on lconway


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 260/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CausalR 1.30.0  (landing page)
Glyn Bradley , Steven Barrett
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/CausalR
git_branch: RELEASE_3_16
git_last_commit: 8f36c59
git_last_commit_date: 2022-11-01 11:11:44 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CausalR
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CausalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CausalR_1.30.0.tar.gz
StartedAt: 2023-04-10 19:14:21 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:15:01 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 40.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CausalR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CausalR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CausalR_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CausalR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.30.0’
* 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-3.16-bioc/meat/CausalR.Rcheck/00check.log’
for details.



Installation output

CausalR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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/Rtmp1Y0Ig2-80623673/corExplainedNodes-filed5052beb66b2.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-80623673/corExplainedNodes-filed5052beb66b2_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp1Y0Ig2-618208007/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-618208007/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/Rtmp1Y0Ig2-793735629/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-793735629/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/Rtmp1Y0Ig2-793735629/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-793735629/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp1Y0Ig2-793735629/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-793735629/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/Rtmp1Y0Ig2/corExplainedNodes-filed5052df737c3.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/corExplainedNodes-filed5052df737c3_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Writing sif file to: /tmp/Rtmp1Y0Ig2/incorExplainedNodes-filed5052df737c3.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/incorExplainedNodes-filed5052df737c3_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp1Y0Ig2/ambExplainedNodes-filed5052df737c3.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/ambExplainedNodes-filed5052df737c3_anno.txt
ambExplainedNodes 

Writing sif file to: /tmp/Rtmp1Y0Ig2/corExplainedNodes-filed505416dfac8.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/corExplainedNodes-filed505416dfac8_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp1Y0Ig2/incorExplainedNodes-filed505416dfac8.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/incorExplainedNodes-filed505416dfac8_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp1Y0Ig2/ambExplainedNodes-filed505416dfac8.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2/ambExplainedNodes-filed505416dfac8_anno.txt
ambExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Inhibits	Node5
Node2	Inhibits	Node5
Writing sif file to: /tmp/Rtmp1Y0Ig2-419887146/corExplainedNodes-filed5051b6b8207.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-419887146/corExplainedNodes-filed5051b6b8207_anno.txt
corExplainedNodes 
Node0	Activates	Node1
Node0	Inhibits	Node2
Node1	Activates	Node3
Node2	Activates	Node6
Node2	Activates	Node7
Writing sif file to: /tmp/Rtmp1Y0Ig2-914373117/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-914373117/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/Rtmp1Y0Ig2-461977636/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-461977636/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/Rtmp1Y0Ig2-461977636/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-461977636/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes 
Node0	Inhibits	Node2
Writing sif file to: /tmp/Rtmp1Y0Ig2-461977636/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/Rtmp1Y0Ig2-461977636/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 10 19:14:52 2023 
*********************************************** 
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 
  1.807   0.650   2.240 

Example timings

CausalR.Rcheck/CausalR-Ex.timings

nameusersystemelapsed
AnalysePredictionsList0.0230.0040.027
CalculateEnrichmentPValue0.0060.0000.007
CalculateSignificance0.0490.0010.051
CalculateSignificanceUsingCubicAlgorithm0.0410.0010.042
CalculateSignificanceUsingCubicAlgorithm1b0.0330.0000.034
CalculateSignificanceUsingQuarticAlgorithm0.0370.0000.038
CompareHypothesis0.0060.0010.007
CreateCCG0.0050.0010.007
CreateCG0.0100.0010.011
GetNodeName0.0070.0000.008
GetNumberOfPositiveAndNegativeEntries0.0010.0010.003
GetShortestPathsFromCCG0.0080.0010.009
MakePredictions0.0070.0010.008
MakePredictionsFromCCG0.0090.0000.010
MakePredictionsFromCG0.0330.0010.034
PlotGraphWithNodeNames0.0590.0020.063
RankTheHypotheses0.1860.1090.257
ReadExperimentalData0.0750.0110.087
ScoreHypothesis0.0020.0000.003
WriteAllExplainedNodesToSifFile0.0930.0930.126
WriteExplainedNodesToSifFile0.0310.0050.037
runSCANR0.3040.1210.377