Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 913/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.12.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2025-10-14 04:45:56 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 05:01:20 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 923.4 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * 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 ‘1.12.0’ * 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 12.978 0.204 13.890 addConnections_TF_peak 8.522 1.756 13.711 addSNPData 8.002 0.747 11.273 plotDiagnosticPlots_peakGene 8.294 0.158 9.689 plotCommunitiesStats 7.770 0.113 8.828 plotCommunitiesEnrichment 7.130 0.197 8.505 plotDiagnosticPlots_TFPeaks 7.116 0.150 8.375 plotGeneralGraphStats 6.076 0.125 6.949 plotPCA_all 5.926 0.171 6.859 calculateCommunitiesEnrichment 5.709 0.234 6.726 visualizeGRN 5.732 0.129 6.620 plotTFEnrichment 4.628 0.091 5.365 plot_stats_connectionSummary 4.258 0.108 5.022 * 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-3.21-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 ‘1.12.0’ ** 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 | 0.000 | 0.001 | 0.001 | |
addConnections_TF_peak | 8.522 | 1.756 | 13.711 | |
addConnections_peak_gene | 3.926 | 0.099 | 4.602 | |
addData | 0.001 | 0.001 | 0.001 | |
addSNPData | 8.002 | 0.747 | 11.273 | |
addTFBS | 0.000 | 0.001 | 0.000 | |
add_TF_gene_correlation | 3.882 | 0.092 | 4.640 | |
add_featureVariation | 0.001 | 0.000 | 0.001 | |
build_eGRN_graph | 2.705 | 0.078 | 3.298 | |
calculateCommunitiesEnrichment | 5.709 | 0.234 | 6.726 | |
calculateCommunitiesStats | 2.811 | 0.069 | 3.424 | |
calculateGeneralEnrichment | 3.228 | 0.112 | 3.799 | |
calculateTFEnrichment | 3.506 | 0.104 | 4.182 | |
changeOutputDirectory | 2.748 | 0.080 | 3.441 | |
deleteIntermediateData | 2.850 | 0.081 | 3.409 | |
filterConnectionsForPlotting | 2.802 | 0.070 | 3.333 | |
filterData | 3.622 | 0.092 | 4.167 | |
filterGRNAndConnectGenes | 2.950 | 0.070 | 3.489 | |
generateStatsSummary | 12.978 | 0.204 | 13.890 | |
getCounts | 2.922 | 0.072 | 3.583 | |
getGRNConnections | 2.835 | 0.082 | 3.449 | |
getGRNSummary | 4.178 | 0.106 | 4.959 | |
getParameters | 3.914 | 0.090 | 4.601 | |
getTopNodes | 3.178 | 0.067 | 3.791 | |
initializeGRN | 0.038 | 0.003 | 0.042 | |
loadExampleObject | 2.745 | 0.068 | 3.375 | |
nGenes | 2.916 | 0.075 | 3.548 | |
nPeaks | 2.956 | 0.076 | 3.629 | |
nTFs | 2.787 | 0.064 | 3.409 | |
overlapPeaksAndTFBS | 2.880 | 0.072 | 3.529 | |
performAllNetworkAnalyses | 0.000 | 0.001 | 0.000 | |
plotCommunitiesEnrichment | 7.130 | 0.197 | 8.505 | |
plotCommunitiesStats | 7.770 | 0.113 | 8.828 | |
plotCorrelations | 3.804 | 0.102 | 4.703 | |
plotDiagnosticPlots_TFPeaks | 7.116 | 0.150 | 8.375 | |
plotDiagnosticPlots_peakGene | 8.294 | 0.158 | 9.689 | |
plotGeneralEnrichment | 3.705 | 0.073 | 4.454 | |
plotGeneralGraphStats | 6.076 | 0.125 | 6.949 | |
plotPCA_all | 5.926 | 0.171 | 6.859 | |
plotTFEnrichment | 4.628 | 0.091 | 5.365 | |
plot_stats_connectionSummary | 4.258 | 0.108 | 5.022 | |
visualizeGRN | 5.732 | 0.129 | 6.620 | |