Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 278/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CausalR 1.37.0 (landing page) Glyn Bradley
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.37.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CausalR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CausalR_1.37.0.tar.gz |
StartedAt: 2024-08-20 23:06:36 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:07:35 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 59.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CausalR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CausalR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CausalR_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CausalR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CausalR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CausalR' version '1.37.0' * 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 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 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 ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/CausalR.Rcheck/00check.log' for details.
CausalR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CausalR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 2 Number of Nodes to analyse: 2 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 2 Number of Nodes to analyse: 2 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 2 Number of Nodes to analyse: 2 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 1 Number of Nodes to analyse: 1 Parallel processing. Number of cores: 2 Number of Nodes to analyse: 3 Number of Nodes to analyse: 3 Parallel processing. Number of cores: 2 [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: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-279288328/corExplainedNodes-file9830f005349.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-279288328/corExplainedNodes-file9830f005349_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-783509528/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-783509528/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: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/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: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-620550250/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/corExplainedNodes-file983072c43388.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/corExplainedNodes-file983072c43388_anno.txt corExplainedNodes Node0 Activates Node1 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/incorExplainedNodes-file983072c43388.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/incorExplainedNodes-file983072c43388_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/ambExplainedNodes-file983072c43388.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/ambExplainedNodes-file983072c43388_anno.txt ambExplainedNodes Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/corExplainedNodes-file98302615591.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/corExplainedNodes-file98302615591_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/incorExplainedNodes-file98302615591.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/incorExplainedNodes-file98302615591_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/ambExplainedNodes-file98302615591.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL/ambExplainedNodes-file98302615591_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-582449164/corExplainedNodes-file9830a54604.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-582449164/corExplainedNodes-file9830a54604_anno.txt corExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Activates Node3 Node2 Activates Node6 Node2 Activates Node7 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-332619127/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-332619127/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: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/corExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/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: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/incorExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt incorExplainedNodes Node0 Inhibits Node2 Writing sif file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+.sif Writing annotation file to: F:/biocbuild/bbs-3.20-bioc/tmpdir/Rtmpo3imVL-794181009/ambExplainedNodes-testNetwork1-testData1-delta2-Node0+_anno.txt ambExplainedNodes Node0 Activates Node1 Node0 Inhibits Node2 Node1 Inhibits Node5 Node2 Inhibits Node5 RUNIT TEST PROTOCOL -- Tue Aug 20 23:07:24 2024 *********************************************** 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 2.04 0.64 12.67
CausalR.Rcheck/CausalR-Ex.timings
name | user | system | elapsed | |
AnalysePredictionsList | 0.00 | 0.01 | 0.02 | |
CalculateEnrichmentPValue | 0 | 0 | 0 | |
CalculateSignificance | 0.03 | 0.00 | 0.03 | |
CalculateSignificanceUsingCubicAlgorithm | 0.03 | 0.02 | 0.05 | |
CalculateSignificanceUsingCubicAlgorithm1b | 0.03 | 0.00 | 0.03 | |
CalculateSignificanceUsingQuarticAlgorithm | 0.05 | 0.00 | 0.04 | |
CompareHypothesis | 0.02 | 0.00 | 0.02 | |
CreateCCG | 0.01 | 0.00 | 0.01 | |
CreateCG | 0.02 | 0.00 | 0.02 | |
GetNodeName | 0 | 0 | 0 | |
GetNumberOfPositiveAndNegativeEntries | 0.01 | 0.00 | 0.02 | |
GetShortestPathsFromCCG | 0 | 0 | 0 | |
MakePredictions | 0.00 | 0.01 | 0.01 | |
MakePredictionsFromCCG | 0.02 | 0.00 | 0.02 | |
MakePredictionsFromCG | 0.03 | 0.00 | 0.03 | |
PlotGraphWithNodeNames | 0.08 | 0.02 | 0.15 | |
RankTheHypotheses | 0.14 | 0.02 | 0.68 | |
ReadExperimentalData | 0.08 | 0.01 | 0.09 | |
ScoreHypothesis | 0 | 0 | 0 | |
WriteAllExplainedNodesToSifFile | 0.04 | 0.03 | 1.23 | |
WriteExplainedNodesToSifFile | 0.04 | 0.03 | 0.07 | |
runSCANR | 0.34 | 0.02 | 1.58 | |