Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 880/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.9.1 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.9.1 |
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_1.9.1.tar.gz |
StartedAt: 2024-06-10 21:28:01 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 21:36:38 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 517.6 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_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.9.1’ * package encoding: UTF-8 * 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 ‘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 8.221 0.233 8.968 plotPCA_all 6.589 0.149 7.161 addConnections_TF_peak 6.002 0.686 7.195 addSNPData 6.407 0.233 8.297 visualizeGRN 5.263 0.108 5.775 plotCommunitiesStats 5.121 0.085 5.578 plotDiagnosticPlots_peakGene 5.020 0.142 5.591 * 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-3.20-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/4.4-arm64/Resources/library’ * installing *source* package ‘GRaNIE’ ... ** 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 | 6.002 | 0.686 | 7.195 | |
addConnections_peak_gene | 4.115 | 0.066 | 4.684 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.407 | 0.233 | 8.297 | |
addTFBS | 0.000 | 0.000 | 0.001 | |
add_TF_gene_correlation | 2.975 | 0.061 | 3.474 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.918 | 0.059 | 3.396 | |
calculateCommunitiesEnrichment | 4.073 | 0.121 | 4.578 | |
calculateCommunitiesStats | 2.666 | 0.071 | 3.130 | |
calculateGeneralEnrichment | 3.124 | 0.059 | 3.552 | |
calculateTFEnrichment | 4.344 | 0.064 | 4.827 | |
changeOutputDirectory | 2.550 | 0.061 | 2.969 | |
deleteIntermediateData | 2.633 | 0.070 | 3.072 | |
filterConnectionsForPlotting | 2.602 | 0.060 | 3.055 | |
filterData | 3.130 | 0.089 | 3.580 | |
filterGRNAndConnectGenes | 2.620 | 0.067 | 3.100 | |
generateStatsSummary | 8.221 | 0.233 | 8.968 | |
getCounts | 2.703 | 0.073 | 3.388 | |
getGRNConnections | 2.596 | 0.075 | 3.083 | |
getGRNSummary | 2.906 | 0.082 | 3.436 | |
getParameters | 2.456 | 0.050 | 2.909 | |
getTopNodes | 2.717 | 0.059 | 3.148 | |
initializeGRN | 0.016 | 0.002 | 0.018 | |
loadExampleObject | 4.067 | 0.065 | 4.563 | |
nGenes | 2.507 | 0.055 | 2.938 | |
nPeaks | 2.613 | 0.067 | 3.078 | |
nTFs | 2.568 | 0.056 | 3.008 | |
overlapPeaksAndTFBS | 2.545 | 0.065 | 3.009 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 4.213 | 0.137 | 4.748 | |
plotCommunitiesStats | 5.121 | 0.085 | 5.578 | |
plotCorrelations | 2.944 | 0.098 | 3.457 | |
plotDiagnosticPlots_TFPeaks | 3.689 | 0.088 | 4.203 | |
plotDiagnosticPlots_peakGene | 5.020 | 0.142 | 5.591 | |
plotGeneralEnrichment | 2.952 | 0.060 | 3.402 | |
plotGeneralGraphStats | 3.614 | 0.059 | 4.069 | |
plotPCA_all | 6.589 | 0.149 | 7.161 | |
plotTFEnrichment | 3.226 | 0.062 | 3.688 | |
plot_stats_connectionSummary | 3.284 | 0.081 | 3.812 | |
visualizeGRN | 5.263 | 0.108 | 5.775 | |