Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 911/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.13.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GRaNIE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.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: GRaNIE |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.13.0.tar.gz |
StartedAt: 2025-09-19 21:24:44 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 21:33:26 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 521.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 37 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘GRaNIE’ 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 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 ... NOTE .performIHW: no visible binding for global variable 'adj_pvalue' Undefined global functions or variables: adj_pvalue * 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateStatsSummary 8.098 0.162 8.754 addConnections_TF_peak 5.703 1.087 9.273 plotDiagnosticPlots_peakGene 6.534 0.141 7.153 plotCommunitiesStats 5.350 0.125 5.915 addSNPData 4.724 0.384 6.613 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘GRaNIE’ ... ** this is package ‘GRaNIE’ version ‘1.13.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (GRaNIE)
GRaNIE.Rcheck/GRaNIE-Ex.timings
name | user | system | elapsed | |
AR_classification_wrapper | 0 | 0 | 0 | |
addConnections_TF_peak | 5.703 | 1.087 | 9.273 | |
addConnections_peak_gene | 2.802 | 0.067 | 3.341 | |
addData | 0 | 0 | 0 | |
addSNPData | 4.724 | 0.384 | 6.613 | |
addTFBS | 0.000 | 0.000 | 0.001 | |
add_TF_gene_correlation | 2.782 | 0.066 | 3.297 | |
add_featureVariation | 0.000 | 0.000 | 0.001 | |
build_eGRN_graph | 1.828 | 0.053 | 2.302 | |
calculateCommunitiesEnrichment | 3.896 | 0.175 | 4.508 | |
calculateCommunitiesStats | 1.976 | 0.053 | 2.493 | |
calculateGeneralEnrichment | 2.240 | 0.072 | 2.748 | |
calculateTFEnrichment | 2.390 | 0.077 | 2.908 | |
changeOutputDirectory | 1.896 | 0.058 | 2.397 | |
deleteIntermediateData | 1.966 | 0.063 | 2.454 | |
filterConnectionsForPlotting | 2.063 | 0.063 | 2.548 | |
filterData | 2.405 | 0.060 | 2.899 | |
filterGRNAndConnectGenes | 2.086 | 0.063 | 2.577 | |
generateStatsSummary | 8.098 | 0.162 | 8.754 | |
getCounts | 2.054 | 0.064 | 2.544 | |
getGRNConnections | 1.925 | 0.069 | 2.442 | |
getGRNSummary | 2.615 | 0.079 | 3.199 | |
getParameters | 1.982 | 0.054 | 2.536 | |
getTopNodes | 2.178 | 0.068 | 2.684 | |
initializeGRN | 0.017 | 0.001 | 0.019 | |
loadExampleObject | 1.930 | 0.051 | 2.415 | |
nGenes | 2.016 | 0.053 | 2.496 | |
nPeaks | 2.170 | 0.058 | 2.713 | |
nTFs | 3.114 | 0.081 | 3.638 | |
overlapPeaksAndTFBS | 1.881 | 0.056 | 2.376 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.586 | 0.130 | 4.191 | |
plotCommunitiesStats | 5.350 | 0.125 | 5.915 | |
plotCorrelations | 2.562 | 0.083 | 3.119 | |
plotDiagnosticPlots_TFPeaks | 3.943 | 0.081 | 4.456 | |
plotDiagnosticPlots_peakGene | 6.534 | 0.141 | 7.153 | |
plotGeneralEnrichment | 2.627 | 0.075 | 3.138 | |
plotGeneralGraphStats | 3.727 | 0.072 | 4.242 | |
plotPCA_all | 4.245 | 0.161 | 4.846 | |
plotTFEnrichment | 2.898 | 0.061 | 3.406 | |
plot_stats_connectionSummary | 2.644 | 0.083 | 3.174 | |
visualizeGRN | 2.756 | 0.102 | 3.284 | |