Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-04 11:37:44 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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 1687/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RCyjs 2.24.0 (landing page) Paul Shannon
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the RCyjs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCyjs.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: RCyjs |
Version: 2.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCyjs_2.24.0.tar.gz |
StartedAt: 2024-03-03 22:51:13 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 22:52:09 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 56.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RCyjs.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCyjs.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCyjs_2.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/RCyjs.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RCyjs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RCyjs’ version ‘2.24.0’ * 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 ‘RCyjs’ 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 startup messages can be suppressed ... 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 ... WARNING Undocumented arguments in documentation object 'hideNodes,RCyjs-method' ‘nodeIDs’ Undocumented arguments in documentation object 'readAndStandardizeJSONNetworkFile' ‘filename’ Documented arguments not in \usage in documentation object 'readAndStandardizeJSONNetworkFile': ‘file’ Undocumented arguments in documentation object 'readAndStandardizeJSONStyleFile' ‘filename’ Documented arguments not in \usage in documentation object 'readAndStandardizeJSONStyleFile': ‘file’ Undocumented arguments in documentation object 'showNodes,RCyjs-method' ‘nodeIDs’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * 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 WARNING See ‘/Users/biocbuild/bbs-3.18-bioc/meat/RCyjs.Rcheck/00check.log’ for details.
RCyjs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RCyjs ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘RCyjs’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘layout’ in package ‘RCyjs’ ** 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 (RCyjs)
RCyjs.Rcheck/tests/runTests.Rout
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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. > # disabled: the bioc build system no longer supports browser use. > # BiocGenerics:::testPackage("RCyjs") > > proc.time() user system elapsed 0.209 0.075 0.277
RCyjs.Rcheck/RCyjs-Ex.timings
name | user | system | elapsed | |
RCyjs-class | 0.001 | 0.001 | 0.001 | |
addGraph | 0.001 | 0.000 | 0.000 | |
addGraphFromFile | 0.001 | 0.001 | 0.001 | |
clearSelection | 0.001 | 0.000 | 0.002 | |
createTestGaph | 0.009 | 0.000 | 0.009 | |
deleteGraph | 0 | 0 | 0 | |
deleteSelectedNodes | 0.001 | 0.000 | 0.002 | |
eda | 0.001 | 0.000 | 0.001 | |
edaNames | 0.001 | 0.001 | 0.001 | |
fit | 0 | 0 | 0 | |
fitSelection | 0 | 0 | 0 | |
getEdgeCount | 0 | 0 | 0 | |
getJSON | 0.000 | 0.000 | 0.001 | |
getLayoutStrategies | 0.000 | 0.000 | 0.001 | |
getNodeCount | 0.000 | 0.000 | 0.001 | |
getNodes | 0 | 0 | 0 | |
getPosition | 0.000 | 0.000 | 0.001 | |
getSelectedNodes | 0 | 0 | 0 | |
getSupportedEdgeDecoratorShapes | 0.000 | 0.000 | 0.001 | |
getSupportedNodeShapes | 0 | 0 | 0 | |
getZoom | 0.000 | 0.000 | 0.001 | |
graphNELtoJSON.string | 0.000 | 0.000 | 0.001 | |
hAlign | 0.001 | 0.001 | 0.001 | |
hideAllEdges | 0.001 | 0.001 | 0.000 | |
hideEdges | 0.001 | 0.001 | 0.001 | |
hideNodes | 0.001 | 0.001 | 0.001 | |
hideSelectedNodes | 0.001 | 0.001 | 0.001 | |
invertNodeSelection | 0.001 | 0.001 | 0.001 | |
layout | 0.001 | 0.001 | 0.001 | |
layoutSelectionInGrid | 0.001 | 0.001 | 0.001 | |
layoutSelectionInGridInferAnchorm | 0.001 | 0.001 | 0.001 | |
loadStyleFile | 0.000 | 0.001 | 0.001 | |
noa | 0.001 | 0.000 | 0.001 | |
noaNames | 0 | 0 | 0 | |
redraw | 0.000 | 0.000 | 0.001 | |
restoreLayout | 0.000 | 0.000 | 0.001 | |
saveJPG | 0.000 | 0.000 | 0.001 | |
saveLayout | 0.000 | 0.000 | 0.001 | |
savePNG | 0.000 | 0.000 | 0.001 | |
selectFirstNeighborsOfSelectedNodes | 0.000 | 0.000 | 0.001 | |
selectNodes | 0 | 0 | 0 | |
setBackgroundColor | 0.000 | 0.000 | 0.001 | |
setDefaultEdgeColor | 0 | 0 | 0 | |
setDefaultEdgeLineColor | 0.001 | 0.000 | 0.000 | |
setDefaultEdgeLineStyle | 0.001 | 0.000 | 0.000 | |
setDefaultEdgeSourceArrowColor | 0.000 | 0.000 | 0.001 | |
setDefaultEdgeSourceArrowShape | 0.000 | 0.001 | 0.001 | |
setDefaultEdgeTargetArrowColor | 0.000 | 0.001 | 0.000 | |
setDefaultEdgeTargetArrowShape | 0.000 | 0.001 | 0.000 | |
setDefaultEdgeWidth | 0.001 | 0.001 | 0.001 | |
setDefaultNodeBorderColor | 0.000 | 0.000 | 0.001 | |
setDefaultNodeBorderWidth | 0 | 0 | 0 | |
setDefaultNodeColor | 0.000 | 0.000 | 0.001 | |
setDefaultNodeFontColor | 0.001 | 0.000 | 0.000 | |
setDefaultNodeFontSize | 0.000 | 0.000 | 0.001 | |
setDefaultNodeHeight | 0.000 | 0.000 | 0.001 | |
setDefaultNodeShape | 0.000 | 0.000 | 0.001 | |
setDefaultNodeSize | 0.000 | 0.000 | 0.001 | |
setDefaultNodeWidth | 0.001 | 0.000 | 0.000 | |
setDefaultStyle | 0.000 | 0.001 | 0.001 | |
setEdgeStyle | 0.000 | 0.001 | 0.001 | |
setGraph | 0 | 0 | 0 | |
setNodeAttributes | 0.001 | 0.000 | 0.001 | |
setNodeBorderColor | 0 | 0 | 0 | |
setNodeBorderWidth | 0.000 | 0.000 | 0.001 | |
setNodeColor | 0.000 | 0.000 | 0.001 | |
setNodeColorRule | 0.000 | 0.000 | 0.001 | |
setNodeFontColor | 0.001 | 0.000 | 0.000 | |
setNodeFontSize | 0 | 0 | 0 | |
setNodeHeight | 0.000 | 0.000 | 0.001 | |
setNodeLabelRule | 0.001 | 0.000 | 0.001 | |
setNodeShape | 0 | 0 | 0 | |
setNodeSize | 0.000 | 0.000 | 0.001 | |
setNodeSizeRule | 0.000 | 0.001 | 0.002 | |
setNodeWidth | 0.001 | 0.001 | 0.001 | |
setPosition | 0.001 | 0.001 | 0.001 | |
setZoom | 0.001 | 0.001 | 0.001 | |
sfn | 0.001 | 0.000 | 0.001 | |
showAll | 0.001 | 0.000 | 0.001 | |
showEdges | 0.001 | 0.000 | 0.004 | |
showNodes | 0.001 | 0.000 | 0.002 | |
simpleDemoGraph | 0.067 | 0.001 | 0.068 | |
vAlign | 0.001 | 0.000 | 0.001 | |