Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-26 11:38 -0400 (Wed, 26 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" | 4691 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4405 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4355 |
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 881/2243 | 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: 2024-06-25 20:40:34 -0400 (Tue, 25 Jun 2024) |
EndedAt: 2024-06-25 20:48:58 -0400 (Tue, 25 Jun 2024) |
EllapsedTime: 503.7 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: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.9.1’ * 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 7.461 0.185 8.132 addSNPData 5.799 0.280 8.170 addConnections_TF_peak 4.650 1.013 8.834 plotPCA_all 5.078 0.166 5.716 * 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-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 | 0.000 | 0.001 | 0.000 | |
addConnections_TF_peak | 4.650 | 1.013 | 8.834 | |
addConnections_peak_gene | 2.910 | 0.071 | 3.467 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.799 | 0.280 | 8.170 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.847 | 0.059 | 2.372 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.987 | 0.065 | 2.504 | |
calculateCommunitiesEnrichment | 3.067 | 0.142 | 3.647 | |
calculateCommunitiesStats | 1.816 | 0.074 | 2.355 | |
calculateGeneralEnrichment | 2.264 | 0.056 | 2.763 | |
calculateTFEnrichment | 3.199 | 0.076 | 3.760 | |
changeOutputDirectory | 1.801 | 0.053 | 2.316 | |
deleteIntermediateData | 1.869 | 0.050 | 2.371 | |
filterConnectionsForPlotting | 1.846 | 0.048 | 2.325 | |
filterData | 2.180 | 0.082 | 2.688 | |
filterGRNAndConnectGenes | 1.880 | 0.054 | 2.390 | |
generateStatsSummary | 7.461 | 0.185 | 8.132 | |
getCounts | 1.948 | 0.068 | 2.469 | |
getGRNConnections | 1.790 | 0.079 | 2.288 | |
getGRNSummary | 2.479 | 0.076 | 2.998 | |
getParameters | 1.680 | 0.045 | 2.203 | |
getTopNodes | 1.846 | 0.055 | 2.384 | |
initializeGRN | 0.017 | 0.002 | 0.020 | |
loadExampleObject | 2.806 | 0.058 | 3.318 | |
nGenes | 1.708 | 0.048 | 2.190 | |
nPeaks | 1.809 | 0.059 | 2.319 | |
nTFs | 1.681 | 0.047 | 2.199 | |
overlapPeaksAndTFBS | 1.738 | 0.063 | 2.292 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.287 | 0.143 | 3.851 | |
plotCommunitiesStats | 4.135 | 0.096 | 4.735 | |
plotCorrelations | 2.198 | 0.096 | 2.760 | |
plotDiagnosticPlots_TFPeaks | 3.375 | 0.078 | 3.942 | |
plotDiagnosticPlots_peakGene | 4.165 | 0.130 | 4.771 | |
plotGeneralEnrichment | 2.088 | 0.055 | 2.615 | |
plotGeneralGraphStats | 2.712 | 0.055 | 3.185 | |
plotPCA_all | 5.078 | 0.166 | 5.716 | |
plotTFEnrichment | 2.402 | 0.058 | 2.901 | |
plot_stats_connectionSummary | 2.461 | 0.080 | 2.981 | |
visualizeGRN | 4.217 | 0.113 | 4.819 | |