Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-02 12:04 -0500 (Mon, 02 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4739 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4482 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4510 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4462 |
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 1690/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RCX 1.10.0 (landing page) Florian Auer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RCX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCX.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: RCX |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCX_1.10.0.tar.gz |
StartedAt: 2024-11-29 05:13:21 -0500 (Fri, 29 Nov 2024) |
EndedAt: 2024-11-29 05:17:56 -0500 (Fri, 29 Nov 2024) |
EllapsedTime: 275.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RCX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCX_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RCX.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘RCX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RCX’ version ‘1.10.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘RCX’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 whether 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 ... NOTE Documented arguments not in \usage in Rd file 'dot-format.Rd': ‘.log’ 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/RCX.Rcheck/00check.log’ for details.
RCX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RCX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘RCX’ ... ** 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 (RCX)
RCX.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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. > library(testthat) > library(RCX) > > test_check("RCX") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 60 ] > > proc.time() user system elapsed 2.105 0.090 2.183
RCX.Rcheck/RCX-Ex.timings
name | user | system | elapsed | |
CartesianLayout | 0.002 | 0.002 | 0.004 | |
Convert-Names-and-Classes | 0.001 | 0.001 | 0.000 | |
CyGroups | 0.003 | 0.000 | 0.004 | |
CyHiddenAttributes | 0.098 | 0.000 | 0.099 | |
CyNetworkRelations | 0.001 | 0.000 | 0.001 | |
CySubNetworks | 0.002 | 0.000 | 0.002 | |
CyTableColumn | 0.004 | 0.000 | 0.004 | |
CyVisualProperties | 0.013 | 0.000 | 0.012 | |
CyVisualProperty | 0.008 | 0.000 | 0.008 | |
CyVisualPropertyDependencies | 0.002 | 0.000 | 0.002 | |
CyVisualPropertyMappings | 0.005 | 0.000 | 0.006 | |
CyVisualPropertyProperties | 0.003 | 0.000 | 0.003 | |
EdgeAttributes | 0.012 | 0.000 | 0.012 | |
Edges | 0.002 | 0.000 | 0.001 | |
Igraph | 2.082 | 0.041 | 2.124 | |
Meta-data | 0.021 | 0.000 | 0.021 | |
NetworkAttributes | 0.012 | 0.000 | 0.011 | |
NodeAttributes | 0.012 | 0.000 | 0.011 | |
Nodes | 0.001 | 0.000 | 0.002 | |
RCX-object | 0.189 | 0.000 | 0.190 | |
aspectClasses | 0 | 0 | 0 | |
checks | 0 | 0 | 0 | |
convert-data-types-and-values | 0.001 | 0.000 | 0.001 | |
convert2json | 0 | 0 | 0 | |
countElements | 0.006 | 0.000 | 0.007 | |
custom-print | 0.004 | 0.001 | 0.004 | |
dot-addAspectNameToJson | 0 | 0 | 0 | |
dot-addAttributeData | 0 | 0 | 0 | |
dot-aspectClass | 0.000 | 0.000 | 0.001 | |
dot-convertRawList | 0.001 | 0.000 | 0.000 | |
dot-createAttributeAspect | 0 | 0 | 0 | |
dot-createCyVpPorD | 0 | 0 | 0 | |
dot-filterBy | 0 | 0 | 0 | |
dot-format | 0 | 0 | 0 | |
dot-infer | 0 | 0 | 0 | |
dot-json2RDataType | 0 | 0 | 0 | |
dot-jsonL | 0 | 0 | 0 | |
dot-jsonV | 0.001 | 0.000 | 0.000 | |
dot-log | 0 | 0 | 0 | |
dot-mergeAttributesAspect | 0 | 0 | 0 | |
dot-mergeIdAspect | 0 | 0 | 0 | |
dot-modClass | 0 | 0 | 0 | |
dot-pasteC | 0 | 0 | 0 | |
dot-renameDF | 0.001 | 0.000 | 0.001 | |
dot-stop | 0 | 0 | 0 | |
dot-summaryAspect | 0.001 | 0.000 | 0.001 | |
dot-transformListLength-set | 0.002 | 0.000 | 0.001 | |
dot-transformVLD | 0.004 | 0.000 | 0.003 | |
getCyVisualProperty | 0.008 | 0.000 | 0.007 | |
graphNEL | 2.245 | 0.006 | 2.250 | |
hasIds | 0.001 | 0.000 | 0.001 | |
idProperty | 0.001 | 0.000 | 0.001 | |
jsonToRCX | 0.001 | 0.001 | 0.002 | |
markAttributeColumn | 0.001 | 0.000 | 0.001 | |
markRefColumn | 0.001 | 0.000 | 0.001 | |
maxId | 0.000 | 0.000 | 0.001 | |
rcxToJson | 0.001 | 0.000 | 0.002 | |
readCX | 0.517 | 0.003 | 0.521 | |
referredBy | 0.006 | 0.000 | 0.007 | |
refersTo | 0.000 | 0.000 | 0.001 | |
setExtension | 0 | 0 | 0 | |
summary | 0.009 | 0.000 | 0.009 | |
toCX | 0.009 | 0.000 | 0.008 | |
updateCartesianLayout | 0.034 | 0.001 | 0.034 | |
updateCyGroups | 0.025 | 0.002 | 0.027 | |
updateCyHiddenAttributes | 0.041 | 0.003 | 0.044 | |
updateCyNetworkRelations | 0.029 | 0.000 | 0.030 | |
updateCySubNetworks | 0.021 | 0.000 | 0.022 | |
updateCyTableColumn | 0.035 | 0.001 | 0.037 | |
updateCyVisualProperties | 0.195 | 0.002 | 0.198 | |
updateCyVisualProperty | 0.05 | 0.00 | 0.05 | |
updateEdgeAttributes | 0.045 | 0.012 | 0.058 | |
updateEdges | 0.015 | 0.003 | 0.019 | |
updateMetaDataProperties | 0.016 | 0.002 | 0.018 | |
updateNetworkAttributes | 0.038 | 0.003 | 0.041 | |
updateNodeAttributes | 0.053 | 0.001 | 0.053 | |
updateNodes | 0.012 | 0.000 | 0.012 | |
validate | 0.216 | 0.004 | 0.219 | |
visualize | 0.007 | 0.000 | 0.006 | |
writeCX | 0 | 0 | 0 | |
writeHTML | 0.043 | 0.014 | 0.063 | |