| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
|
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 272/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CausalR 1.31.0 (landing page) Glyn Bradley
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: CausalR |
| Version: 1.31.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CausalR_1.31.0.tar.gz |
| StartedAt: 2023-04-11 19:05:44 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 19:06:33 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 49.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CausalR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CausalR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CausalR_1.31.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CausalR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CausalR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CausalR’ version ‘1.31.0’
* 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-3.17-bioc/meat/CausalR.Rcheck/00check.log’
for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CausalR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 alpha (2023-04-03 r84154)
Copyright (C) 2023 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/RtmpS0WtHd-480596189/corExplainedNodes-file130619785ef21b.sif
Writing annotation file to: /tmp/RtmpS0WtHd-480596189/corExplainedNodes-file130619785ef21b_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpS0WtHd-763653588/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-763653588/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/RtmpS0WtHd-320568970/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-320568970/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/RtmpS0WtHd-320568970/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-320568970/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpS0WtHd-320568970/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-320568970/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/RtmpS0WtHd/corExplainedNodes-file130619146050bb.sif
Writing annotation file to: /tmp/RtmpS0WtHd/corExplainedNodes-file130619146050bb_anno.txt
corExplainedNodes
Node0 Activates Node1
Writing sif file to: /tmp/RtmpS0WtHd/incorExplainedNodes-file130619146050bb.sif
Writing annotation file to: /tmp/RtmpS0WtHd/incorExplainedNodes-file130619146050bb_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpS0WtHd/ambExplainedNodes-file130619146050bb.sif
Writing annotation file to: /tmp/RtmpS0WtHd/ambExplainedNodes-file130619146050bb_anno.txt
ambExplainedNodes
Writing sif file to: /tmp/RtmpS0WtHd/corExplainedNodes-file13061930c79de7.sif
Writing annotation file to: /tmp/RtmpS0WtHd/corExplainedNodes-file13061930c79de7_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpS0WtHd/incorExplainedNodes-file13061930c79de7.sif
Writing annotation file to: /tmp/RtmpS0WtHd/incorExplainedNodes-file13061930c79de7_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpS0WtHd/ambExplainedNodes-file13061930c79de7.sif
Writing annotation file to: /tmp/RtmpS0WtHd/ambExplainedNodes-file13061930c79de7_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
Writing sif file to: /tmp/RtmpS0WtHd-55942426/corExplainedNodes-file1306196d98e980.sif
Writing annotation file to: /tmp/RtmpS0WtHd-55942426/corExplainedNodes-file1306196d98e980_anno.txt
corExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Activates Node3
Node2 Activates Node6
Node2 Activates Node7
Writing sif file to: /tmp/RtmpS0WtHd-483805971/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-483805971/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/RtmpS0WtHd-66064163/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-66064163/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/RtmpS0WtHd-66064163/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-66064163/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
incorExplainedNodes
Node0 Inhibits Node2
Writing sif file to: /tmp/RtmpS0WtHd-66064163/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif
Writing annotation file to: /tmp/RtmpS0WtHd-66064163/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt
ambExplainedNodes
Node0 Activates Node1
Node0 Inhibits Node2
Node1 Inhibits Node5
Node2 Inhibits Node5
RUNIT TEST PROTOCOL -- Tue Apr 11 19:06:05 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
1.646 0.339 1.807
CausalR.Rcheck/CausalR-Ex.timings
| name | user | system | elapsed | |
| AnalysePredictionsList | 0.02 | 0.00 | 0.02 | |
| CalculateEnrichmentPValue | 0.002 | 0.000 | 0.002 | |
| CalculateSignificance | 0.046 | 0.000 | 0.047 | |
| CalculateSignificanceUsingCubicAlgorithm | 0.042 | 0.000 | 0.042 | |
| CalculateSignificanceUsingCubicAlgorithm1b | 0.038 | 0.000 | 0.038 | |
| CalculateSignificanceUsingQuarticAlgorithm | 0.041 | 0.000 | 0.042 | |
| CompareHypothesis | 0.009 | 0.000 | 0.008 | |
| CreateCCG | 0.002 | 0.004 | 0.005 | |
| CreateCG | 0.005 | 0.000 | 0.006 | |
| GetNodeName | 0.005 | 0.000 | 0.006 | |
| GetNumberOfPositiveAndNegativeEntries | 0.001 | 0.000 | 0.001 | |
| GetShortestPathsFromCCG | 0.007 | 0.000 | 0.007 | |
| MakePredictions | 0.008 | 0.000 | 0.009 | |
| MakePredictionsFromCCG | 0.002 | 0.004 | 0.006 | |
| MakePredictionsFromCG | 0.031 | 0.000 | 0.032 | |
| PlotGraphWithNodeNames | 0.054 | 0.004 | 0.058 | |
| RankTheHypotheses | 0.065 | 0.025 | 0.065 | |
| ReadExperimentalData | 0.006 | 0.004 | 0.010 | |
| ScoreHypothesis | 0.002 | 0.000 | 0.002 | |
| WriteAllExplainedNodesToSifFile | 0.129 | 0.063 | 0.143 | |
| WriteExplainedNodesToSifFile | 0.088 | 0.000 | 0.088 | |
| runSCANR | 0.320 | 0.073 | 0.339 | |