Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-27 11:37:40 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4667 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4403 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4426 |
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 894/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.6.1 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / 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: 1.6.1 |
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_1.6.1.tar.gz |
StartedAt: 2024-03-26 03:27:11 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 03:41:44 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 872.4 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_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.6.1’ * 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' 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 11.942 0.193 13.191 plotDiagnosticPlots_peakGene 9.211 0.229 10.120 addConnections_TF_peak 7.171 1.232 10.706 addSNPData 7.050 0.340 16.103 plotDiagnosticPlots_TFPeaks 6.426 0.236 7.168 visualizeGRN 6.272 0.105 7.022 plotCommunitiesEnrichment 6.052 0.178 7.137 plotGeneralGraphStats 5.815 0.105 6.835 plot_stats_connectionSummary 5.372 0.106 6.084 plotCommunitiesStats 5.257 0.187 6.054 getGRNSummary 5.153 0.112 5.914 plotCorrelations 5.030 0.156 5.809 filterData 4.773 0.096 5.586 calculateCommunitiesEnrichment 4.728 0.120 6.103 plotTFEnrichment 4.610 0.091 5.548 plotPCA_all 4.485 0.164 5.487 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-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 ** 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 | 0.000 | |
addConnections_TF_peak | 7.171 | 1.232 | 10.706 | |
addConnections_peak_gene | 3.908 | 0.092 | 4.713 | |
addData | 0.001 | 0.000 | 0.001 | |
addSNPData | 7.050 | 0.340 | 16.103 | |
addTFBS | 0.000 | 0.001 | 0.001 | |
add_TF_gene_correlation | 2.957 | 0.080 | 3.585 | |
add_featureVariation | 0.001 | 0.000 | 0.001 | |
build_eGRN_graph | 3.897 | 0.091 | 4.652 | |
calculateCommunitiesEnrichment | 4.728 | 0.120 | 6.103 | |
calculateCommunitiesStats | 3.079 | 0.084 | 4.142 | |
calculateGeneralEnrichment | 3.429 | 0.072 | 4.346 | |
calculateTFEnrichment | 3.641 | 0.079 | 4.411 | |
changeOutputDirectory | 3.002 | 0.083 | 3.801 | |
deleteIntermediateData | 2.851 | 0.072 | 3.600 | |
filterConnectionsForPlotting | 2.980 | 0.069 | 3.728 | |
filterData | 4.773 | 0.096 | 5.586 | |
filterGRNAndConnectGenes | 2.984 | 0.073 | 3.580 | |
generateStatsSummary | 11.942 | 0.193 | 13.191 | |
getCounts | 3.149 | 0.093 | 3.797 | |
getGRNConnections | 2.921 | 0.072 | 3.553 | |
getGRNSummary | 5.153 | 0.112 | 5.914 | |
getParameters | 2.936 | 0.081 | 3.666 | |
getTopNodes | 3.030 | 0.072 | 3.844 | |
initializeGRN | 0.036 | 0.003 | 0.039 | |
loadExampleObject | 3.971 | 0.079 | 4.678 | |
nGenes | 2.839 | 0.070 | 3.524 | |
nPeaks | 2.909 | 0.069 | 3.547 | |
nTFs | 2.911 | 0.071 | 3.616 | |
overlapPeaksAndTFBS | 2.864 | 0.063 | 3.549 | |
performAllNetworkAnalyses | 0.000 | 0.001 | 0.001 | |
plotCommunitiesEnrichment | 6.052 | 0.178 | 7.137 | |
plotCommunitiesStats | 5.257 | 0.187 | 6.054 | |
plotCorrelations | 5.030 | 0.156 | 5.809 | |
plotDiagnosticPlots_TFPeaks | 6.426 | 0.236 | 7.168 | |
plotDiagnosticPlots_peakGene | 9.211 | 0.229 | 10.120 | |
plotGeneralEnrichment | 3.639 | 0.076 | 4.313 | |
plotGeneralGraphStats | 5.815 | 0.105 | 6.835 | |
plotPCA_all | 4.485 | 0.164 | 5.487 | |
plotTFEnrichment | 4.610 | 0.091 | 5.548 | |
plot_stats_connectionSummary | 5.372 | 0.106 | 6.084 | |
visualizeGRN | 6.272 | 0.105 | 7.022 | |