Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-21 13:23 -0400 (Fri, 21 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" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 881/2242 | 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 | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 2024-06-20 21:19:21 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 21:22:13 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 171.9 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 4.4.1 RC (2024-06-06 r86719) * 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 13.6.5 * 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 * 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 | 1.618 | 0.186 | 3.115 | |
addConnections_peak_gene | 1.121 | 0.014 | 1.590 | |
addData | 0 | 0 | 0 | |
addSNPData | 1.803 | 0.063 | 3.825 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 0.764 | 0.015 | 1.199 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 0.761 | 0.017 | 1.220 | |
calculateCommunitiesEnrichment | 1.029 | 0.034 | 1.486 | |
calculateCommunitiesStats | 1.160 | 0.021 | 1.607 | |
calculateGeneralEnrichment | 0.774 | 0.015 | 1.238 | |
calculateTFEnrichment | 0.849 | 0.016 | 1.274 | |
changeOutputDirectory | 0.717 | 0.019 | 1.198 | |
deleteIntermediateData | 0.658 | 0.019 | 1.117 | |
filterConnectionsForPlotting | 0.604 | 0.015 | 1.055 | |
filterData | 0.859 | 0.023 | 1.334 | |
filterGRNAndConnectGenes | 0.717 | 0.025 | 1.138 | |
generateStatsSummary | 2.625 | 0.072 | 3.199 | |
getCounts | 0.676 | 0.023 | 1.129 | |
getGRNConnections | 1.100 | 0.026 | 1.584 | |
getGRNSummary | 0.805 | 0.021 | 1.250 | |
getParameters | 0.678 | 0.021 | 1.116 | |
getTopNodes | 0.687 | 0.016 | 1.172 | |
initializeGRN | 0.005 | 0.001 | 0.006 | |
loadExampleObject | 0.722 | 0.020 | 1.184 | |
nGenes | 0.681 | 0.020 | 1.151 | |
nPeaks | 0.698 | 0.016 | 1.159 | |
nTFs | 0.705 | 0.021 | 1.150 | |
overlapPeaksAndTFBS | 0.720 | 0.015 | 1.197 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 1.189 | 0.042 | 1.659 | |
plotCommunitiesStats | 0.946 | 0.023 | 1.420 | |
plotCorrelations | 1.204 | 0.030 | 1.671 | |
plotDiagnosticPlots_TFPeaks | 1.096 | 0.022 | 1.548 | |
plotDiagnosticPlots_peakGene | 1.800 | 0.059 | 2.310 | |
plotGeneralEnrichment | 0.750 | 0.018 | 1.193 | |
plotGeneralGraphStats | 0.948 | 0.020 | 1.447 | |
plotPCA_all | 1.517 | 0.058 | 2.021 | |
plotTFEnrichment | 0.937 | 0.022 | 1.409 | |
plot_stats_connectionSummary | 0.926 | 0.025 | 1.442 | |
visualizeGRN | 1.088 | 0.041 | 1.540 | |