Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-10-16 11:37:06 -0400 (Mon, 16 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
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 873/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.4.1 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
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: 1.4.1 |
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_1.4.1.tar.gz |
StartedAt: 2023-10-16 02:22:27 -0400 (Mon, 16 Oct 2023) |
EndedAt: 2023-10-16 02:39:13 -0400 (Mon, 16 Oct 2023) |
EllapsedTime: 1006.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.4.1’ * 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 R 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 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' getGRNSummary: no visible binding for global variable 'pval' Undefined global functions or variables: adj_pvalue pval * checking Rd files ... OK * checking Rd metadata ... WARNING Rd files with duplicated name 'nGenes': ‘genes-methods.Rd’ ‘nGenes.Rd’ Rd files with duplicated name 'nPeaks': ‘nPeaks.Rd’ ‘peaks-methods.Rd’ Rd files with duplicated alias 'genes': ‘genes-methods.Rd’ ‘nGenes.Rd’ Rd files with duplicated alias 'nGenes': ‘genes-methods.Rd’ ‘nGenes.Rd’ Rd files with duplicated alias 'nPeaks': ‘nPeaks.Rd’ ‘peaks-methods.Rd’ Rd files with duplicated alias 'peaks': ‘nPeaks.Rd’ ‘peaks-methods.Rd’ * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Functions or methods with usage in documentation object 'installSuggestedPackages' but not in code: 'installSuggestedPackages' * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed generateStatsSummary 13.226 0.192 17.233 plotDiagnosticPlots_peakGene 8.930 0.174 11.886 addConnections_TF_peak 6.918 1.380 11.026 plotDiagnosticPlots_TFPeaks 6.415 0.119 8.712 plotCommunitiesEnrichment 5.978 0.169 8.202 calculateCommunitiesEnrichment 5.920 0.146 7.964 plotGeneralGraphStats 5.301 0.370 8.157 plotCommunitiesStats 5.396 0.093 7.575 getGRNSummary 5.355 0.118 7.455 plotTFEnrichment 4.891 0.087 7.071 visualizeGRN 4.814 0.105 6.937 calculateTFEnrichment 4.816 0.089 6.422 plotPCA_all 4.442 0.192 6.864 plot_stats_connectionSummary 4.349 0.123 6.667 filterGRNAndConnectGenes 4.012 0.098 5.456 nPeaks 4.007 0.089 5.723 peaks-methods 4.003 0.088 5.706 addConnections_peak_gene 3.987 0.098 5.558 filterData 3.674 0.091 5.305 plotCorrelations 3.651 0.104 5.326 plotGeneralEnrichment 3.541 0.122 5.130 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.17-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/4.3-x86_64/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 | 0.001 | 0.000 | 0.001 | |
addConnections_TF_peak | 6.918 | 1.380 | 11.026 | |
addConnections_peak_gene | 3.987 | 0.098 | 5.558 | |
addData | 0.000 | 0.000 | 0.001 | |
addTFBS | 0.000 | 0.001 | 0.001 | |
add_TF_gene_correlation | 2.812 | 0.091 | 4.000 | |
add_featureVariation | 0.000 | 0.000 | 0.001 | |
build_eGRN_graph | 2.883 | 0.081 | 4.037 | |
calculateCommunitiesEnrichment | 5.920 | 0.146 | 7.964 | |
calculateCommunitiesStats | 2.876 | 0.076 | 3.979 | |
calculateGeneralEnrichment | 3.534 | 0.125 | 4.823 | |
calculateTFEnrichment | 4.816 | 0.089 | 6.422 | |
changeOutputDirectory | 2.857 | 0.072 | 4.131 | |
deleteIntermediateData | 2.962 | 0.077 | 4.175 | |
filterData | 3.674 | 0.091 | 5.305 | |
filterGRNAndConnectGenes | 4.012 | 0.098 | 5.456 | |
generateStatsSummary | 13.226 | 0.192 | 17.233 | |
genes-methods | 2.836 | 0.075 | 4.076 | |
getCounts | 3.162 | 0.098 | 4.659 | |
getGRNConnections | 2.842 | 0.071 | 4.093 | |
getGRNSummary | 5.355 | 0.118 | 7.455 | |
getParameters | 2.846 | 0.083 | 4.334 | |
getTopNodes | 3.099 | 0.097 | 4.544 | |
initializeGRN | 0.040 | 0.008 | 0.064 | |
installSuggestedPackages | 0.000 | 0.000 | 0.001 | |
loadExampleObject | 3.008 | 0.116 | 4.538 | |
nGenes | 3.022 | 0.090 | 4.600 | |
nPeaks | 4.007 | 0.089 | 5.723 | |
nTFs | 2.829 | 0.066 | 4.246 | |
overlapPeaksAndTFBS | 2.935 | 0.071 | 4.297 | |
peaks-methods | 4.003 | 0.088 | 5.706 | |
performAllNetworkAnalyses | 0.001 | 0.000 | 0.000 | |
plotCommunitiesEnrichment | 5.978 | 0.169 | 8.202 | |
plotCommunitiesStats | 5.396 | 0.093 | 7.575 | |
plotCorrelations | 3.651 | 0.104 | 5.326 | |
plotDiagnosticPlots_TFPeaks | 6.415 | 0.119 | 8.712 | |
plotDiagnosticPlots_peakGene | 8.930 | 0.174 | 11.886 | |
plotGeneralEnrichment | 3.541 | 0.122 | 5.130 | |
plotGeneralGraphStats | 5.301 | 0.370 | 8.157 | |
plotPCA_all | 4.442 | 0.192 | 6.864 | |
plotTFEnrichment | 4.891 | 0.087 | 7.071 | |
plot_stats_connectionSummary | 4.349 | 0.123 | 6.667 | |
visualizeGRN | 4.814 | 0.105 | 6.937 | |