| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:27 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 269/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CausalR 1.33.0 (landing page) Glyn Bradley
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: CausalR |
| Version: 1.33.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CausalR_1.33.0.tar.gz |
| StartedAt: 2023-06-05 18:55:06 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 18:56:02 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 56.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CausalR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CausalR_1.33.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CausalR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.33.0’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘CausalR.rnw’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/CausalR.Rcheck/00check.log’
for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CausalR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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/RtmpIbm2uW-774363001/corExplainedNodes-file17b4412e40de3a.sif
Writing annotation file to: /tmp/RtmpIbm2uW-774363001/corExplainedNodes-file17b4412e40de3a_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIbm2uW-719381266/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-719381266/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/RtmpIbm2uW-327655013/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-327655013/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/RtmpIbm2uW-327655013/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-327655013/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIbm2uW-327655013/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-327655013/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/RtmpIbm2uW/corExplainedNodes-file17b4412f56e902.sif
Writing annotation file to: /tmp/RtmpIbm2uW/corExplainedNodes-file17b4412f56e902_anno.txt
corExplainedNodes
Node0 Activates Node1
Writing sif file to: /tmp/RtmpIbm2uW/incorExplainedNodes-file17b4412f56e902.sif
Writing annotation file to: /tmp/RtmpIbm2uW/incorExplainedNodes-file17b4412f56e902_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIbm2uW/ambExplainedNodes-file17b4412f56e902.sif
Writing annotation file to: /tmp/RtmpIbm2uW/ambExplainedNodes-file17b4412f56e902_anno.txt
ambExplainedNodes
Writing sif file to: /tmp/RtmpIbm2uW/corExplainedNodes-file17b4415c270622.sif
Writing annotation file to: /tmp/RtmpIbm2uW/corExplainedNodes-file17b4415c270622_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIbm2uW/incorExplainedNodes-file17b4415c270622.sif
Writing annotation file to: /tmp/RtmpIbm2uW/incorExplainedNodes-file17b4415c270622_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIbm2uW/ambExplainedNodes-file17b4415c270622.sif
Writing annotation file to: /tmp/RtmpIbm2uW/ambExplainedNodes-file17b4415c270622_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
Writing sif file to: /tmp/RtmpIbm2uW-138125120/corExplainedNodes-file17b441f47de1b.sif
Writing annotation file to: /tmp/RtmpIbm2uW-138125120/corExplainedNodes-file17b441f47de1b_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpIbm2uW-219080258/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-219080258/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/RtmpIbm2uW-811781343/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-811781343/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/RtmpIbm2uW-811781343/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-811781343/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpIbm2uW-811781343/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpIbm2uW-811781343/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
RUNIT TEST PROTOCOL -- Mon Jun 5 18:55:37 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
2.253 0.586 2.641
CausalR.Rcheck/CausalR-Ex.timings
| name | user | system | elapsed | |
| AnalysePredictionsList | 0.026 | 0.001 | 0.028 | |
| CalculateEnrichmentPValue | 0.007 | 0.000 | 0.008 | |
| CalculateSignificance | 0.074 | 0.000 | 0.073 | |
| CalculateSignificanceUsingCubicAlgorithm | 0.076 | 0.000 | 0.075 | |
| CalculateSignificanceUsingCubicAlgorithm1b | 0.064 | 0.000 | 0.064 | |
| CalculateSignificanceUsingQuarticAlgorithm | 0.071 | 0.000 | 0.071 | |
| CompareHypothesis | 0.007 | 0.000 | 0.007 | |
| CreateCCG | 0.013 | 0.000 | 0.013 | |
| CreateCG | 0.007 | 0.000 | 0.006 | |
| GetNodeName | 0.009 | 0.000 | 0.008 | |
| GetNumberOfPositiveAndNegativeEntries | 0.002 | 0.000 | 0.003 | |
| GetShortestPathsFromCCG | 0.009 | 0.000 | 0.010 | |
| MakePredictions | 0.010 | 0.003 | 0.014 | |
| MakePredictionsFromCCG | 0.009 | 0.001 | 0.009 | |
| MakePredictionsFromCG | 0.045 | 0.000 | 0.045 | |
| PlotGraphWithNodeNames | 0.069 | 0.000 | 0.069 | |
| RankTheHypotheses | 0.133 | 0.048 | 0.148 | |
| ReadExperimentalData | 0.017 | 0.001 | 0.017 | |
| ScoreHypothesis | 0.004 | 0.000 | 0.004 | |
| WriteAllExplainedNodesToSifFile | 0.169 | 0.063 | 0.181 | |
| WriteExplainedNodesToSifFile | 0.046 | 0.000 | 0.046 | |
| runSCANR | 0.382 | 0.072 | 0.403 | |