Glyn Bradley
| Snapshot Date: 2025-10-21 13:45 -0400 (Tue, 21 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/CausalR |
| git_branch: devel |
| git_last_commit: 8c41ab1 |
| git_last_commit_date: 2025-04-15 10:51:17 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-22 12:03 -0400 (Wed, 22 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4890 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4680 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4625 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 | ||||
| Package 289/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CausalR 1.41.0 (landing page) Glyn Bradley
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CausalR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: CausalR |
| Version: 1.41.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CausalR_1.41.0.tar.gz |
| StartedAt: 2025-10-21 21:51:54 -0400 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 21:52:33 -0400 (Tue, 21 Oct 2025) |
| EllapsedTime: 39.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CausalR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CausalR_1.41.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CausalR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.41.0’
* 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 code 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 loading without being on the library search path ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/CausalR.Rcheck/00check.log’
for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CausalR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘CausalR’ ... ** this is package ‘CausalR’ version ‘1.41.0’ ** 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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/RtmpZAfGog-902081245/corExplainedNodes-file25846143bcff56.sif
Writing annotation file to: /tmp/RtmpZAfGog-902081245/corExplainedNodes-file25846143bcff56_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpZAfGog-327977275/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-327977275/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/RtmpZAfGog-512065983/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-512065983/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/RtmpZAfGog-512065983/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-512065983/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpZAfGog-512065983/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-512065983/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/RtmpZAfGog/corExplainedNodes-file25846164860010.sif
Writing annotation file to: /tmp/RtmpZAfGog/corExplainedNodes-file25846164860010_anno.txt
corExplainedNodes
Node0 Activates Node1
Writing sif file to: /tmp/RtmpZAfGog/incorExplainedNodes-file25846164860010.sif
Writing annotation file to: /tmp/RtmpZAfGog/incorExplainedNodes-file25846164860010_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpZAfGog/ambExplainedNodes-file25846164860010.sif
Writing annotation file to: /tmp/RtmpZAfGog/ambExplainedNodes-file25846164860010_anno.txt
ambExplainedNodes
Writing sif file to: /tmp/RtmpZAfGog/corExplainedNodes-file25846121d0fcca.sif
Writing annotation file to: /tmp/RtmpZAfGog/corExplainedNodes-file25846121d0fcca_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpZAfGog/incorExplainedNodes-file25846121d0fcca.sif
Writing annotation file to: /tmp/RtmpZAfGog/incorExplainedNodes-file25846121d0fcca_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpZAfGog/ambExplainedNodes-file25846121d0fcca.sif
Writing annotation file to: /tmp/RtmpZAfGog/ambExplainedNodes-file25846121d0fcca_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
Writing sif file to: /tmp/RtmpZAfGog-71204160/corExplainedNodes-file25846116d5660f.sif
Writing annotation file to: /tmp/RtmpZAfGog-71204160/corExplainedNodes-file25846116d5660f_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpZAfGog-423346933/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-423346933/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/RtmpZAfGog-557190050/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-557190050/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/RtmpZAfGog-557190050/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-557190050/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpZAfGog-557190050/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpZAfGog-557190050/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
RUNIT TEST PROTOCOL -- Tue Oct 21 21:52:16 2025
***********************************************
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
1.707 0.438 1.914
CausalR.Rcheck/CausalR-Ex.timings
| name | user | system | elapsed | |
| AnalysePredictionsList | 0.021 | 0.001 | 0.022 | |
| CalculateEnrichmentPValue | 0.002 | 0.000 | 0.002 | |
| CalculateSignificance | 0.043 | 0.000 | 0.043 | |
| CalculateSignificanceUsingCubicAlgorithm | 0.04 | 0.00 | 0.04 | |
| CalculateSignificanceUsingCubicAlgorithm1b | 0.036 | 0.000 | 0.036 | |
| CalculateSignificanceUsingQuarticAlgorithm | 0.042 | 0.000 | 0.042 | |
| CompareHypothesis | 0.005 | 0.000 | 0.005 | |
| CreateCCG | 0.004 | 0.001 | 0.005 | |
| CreateCG | 0.005 | 0.000 | 0.004 | |
| GetNodeName | 0.005 | 0.000 | 0.005 | |
| GetNumberOfPositiveAndNegativeEntries | 0.001 | 0.000 | 0.002 | |
| GetShortestPathsFromCCG | 0.009 | 0.001 | 0.010 | |
| MakePredictions | 0.006 | 0.000 | 0.006 | |
| MakePredictionsFromCCG | 0.006 | 0.000 | 0.006 | |
| MakePredictionsFromCG | 0.048 | 0.000 | 0.047 | |
| PlotGraphWithNodeNames | 0.072 | 0.001 | 0.074 | |
| RankTheHypotheses | 0.164 | 0.028 | 0.169 | |
| ReadExperimentalData | 0.009 | 0.001 | 0.010 | |
| ScoreHypothesis | 0.003 | 0.000 | 0.003 | |
| WriteAllExplainedNodesToSifFile | 0.071 | 0.060 | 0.087 | |
| WriteExplainedNodesToSifFile | 0.036 | 0.005 | 0.040 | |
| runSCANR | 0.335 | 0.071 | 0.360 | |